Starting phenix.real_space_refine on Fri Mar 6 17:05:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot2_20192/03_2026/6ot2_20192.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 11344 2.51 5 N 3000 2.21 5 O 2932 1.98 5 H 14975 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32311 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 8077 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 613} Chain breaks: 4 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'UNK:plan-1': 14, 'GLU:plan': 42, 'GLN:plan1': 11, 'ARG:plan': 15, 'ASP:plan': 18, 'PHE:plan': 9, 'ASN:plan1': 11, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 468 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 8077 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 613} Chain breaks: 4 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'UNK:plan-1': 14, 'GLU:plan': 42, 'GLN:plan1': 11, 'ARG:plan': 15, 'ASP:plan': 18, 'PHE:plan': 9, 'ASN:plan1': 11, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 468 Chain: "D" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 8080 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 613} Chain breaks: 4 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'UNK:plan-1': 14, 'GLU:plan': 42, 'GLN:plan1': 11, 'ARG:plan': 15, 'ASP:plan': 18, 'PHE:plan': 9, 'ASN:plan1': 11, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 468 Chain: "C" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 8077 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 11, 'TRANS': 613} Chain breaks: 4 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 610 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'UNK:plan-1': 14, 'GLU:plan': 42, 'GLN:plan1': 11, 'ARG:plan': 15, 'ASP:plan': 18, 'PHE:plan': 9, 'ASN:plan1': 11, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 468 Time building chain proxies: 6.44, per 1000 atoms: 0.20 Number of scatterers: 32311 At special positions: 0 Unit cell: (140.98, 140.98, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 O 2932 8.00 N 3000 7.00 C 11344 6.00 H 14975 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4784 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 70.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 111 through 130 Processing helix chain 'A' and resid 132 through 149 Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.903A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 removed outlier: 3.518A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.997A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 461 removed outlier: 5.637A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.622A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 3.555A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.533A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 removed outlier: 3.850A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.804A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 4.044A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 680 removed outlier: 3.635A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.716A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.903A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.519A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 315 through 328 removed outlier: 3.997A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 422 through 461 removed outlier: 5.637A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.622A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.555A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.533A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 removed outlier: 3.850A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.805A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 609 removed outlier: 4.045A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 680 removed outlier: 3.636A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 678 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.716A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.904A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 239 removed outlier: 3.518A pdb=" N GLY D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 315 through 328 removed outlier: 3.997A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 422 through 461 removed outlier: 5.638A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.622A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.555A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.533A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 568 removed outlier: 3.851A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.804A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 609 removed outlier: 4.045A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 680 removed outlier: 3.636A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 678 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 Processing helix chain 'D' and resid 708 through 716 Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.716A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 130 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.903A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.519A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.997A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 422 through 461 removed outlier: 5.638A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.622A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 3.555A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.532A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 568 removed outlier: 3.851A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.803A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 609 removed outlier: 4.045A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 680 removed outlier: 3.636A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 678 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.716A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 3.622A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 3.622A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 377 through 382 removed outlier: 3.622A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 377 through 382 removed outlier: 3.622A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14967 1.02 - 1.22: 12 1.22 - 1.41: 7431 1.41 - 1.61: 10157 1.61 - 1.81: 100 Bond restraints: 32667 Sorted by residual: bond pdb=" ND2 ASN B 415 " pdb="HD21 ASN B 415 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 415 " pdb="HD22 ASN B 415 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN D 415 " pdb="HD21 ASN D 415 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN C 415 " pdb="HD21 ASN C 415 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN C 415 " pdb="HD22 ASN C 415 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 ... (remaining 32662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 55619 1.79 - 3.58: 2462 3.58 - 5.38: 197 5.38 - 7.17: 32 7.17 - 8.96: 12 Bond angle restraints: 58322 Sorted by residual: angle pdb=" C GLU B 308 " pdb=" N ASP B 309 " pdb=" CA ASP B 309 " ideal model delta sigma weight residual 121.86 130.82 -8.96 1.65e+00 3.67e-01 2.95e+01 angle pdb=" C GLU D 308 " pdb=" N ASP D 309 " pdb=" CA ASP D 309 " ideal model delta sigma weight residual 121.86 130.81 -8.95 1.65e+00 3.67e-01 2.94e+01 angle pdb=" C GLU C 308 " pdb=" N ASP C 309 " pdb=" CA ASP C 309 " ideal model delta sigma weight residual 121.86 130.80 -8.94 1.65e+00 3.67e-01 2.93e+01 angle pdb=" C GLU A 308 " pdb=" N ASP A 309 " pdb=" CA ASP A 309 " ideal model delta sigma weight residual 121.86 130.79 -8.93 1.65e+00 3.67e-01 2.93e+01 angle pdb=" C ARG B 319 " pdb=" N MET B 320 " pdb=" CA MET B 320 " ideal model delta sigma weight residual 120.28 126.39 -6.11 1.34e+00 5.57e-01 2.08e+01 ... (remaining 58317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 14590 15.81 - 31.61: 967 31.61 - 47.42: 196 47.42 - 63.23: 120 63.23 - 79.03: 8 Dihedral angle restraints: 15881 sinusoidal: 7205 harmonic: 8676 Sorted by residual: dihedral pdb=" CA UNK D 4 " pdb=" C UNK D 4 " pdb=" N UNK D 5 " pdb=" CA UNK D 5 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA UNK B 4 " pdb=" C UNK B 4 " pdb=" N UNK B 5 " pdb=" CA UNK B 5 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA UNK A 4 " pdb=" C UNK A 4 " pdb=" N UNK A 5 " pdb=" CA UNK A 5 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1725 0.031 - 0.062: 752 0.062 - 0.093: 365 0.093 - 0.124: 118 0.124 - 0.155: 44 Chirality restraints: 3004 Sorted by residual: chirality pdb=" CA GLU A 308 " pdb=" N GLU A 308 " pdb=" C GLU A 308 " pdb=" CB GLU A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA GLU C 308 " pdb=" N GLU C 308 " pdb=" C GLU C 308 " pdb=" CB GLU C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA GLU B 308 " pdb=" N GLU B 308 " pdb=" C GLU B 308 " pdb=" CB GLU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3001 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 319 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" N MET B 320 " -0.051 2.00e-02 2.50e+03 pdb=" CA MET B 320 " 0.014 2.00e-02 2.50e+03 pdb=" H MET B 320 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 319 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" N MET C 320 " -0.051 2.00e-02 2.50e+03 pdb=" CA MET C 320 " 0.014 2.00e-02 2.50e+03 pdb=" H MET C 320 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 319 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" N MET D 320 " -0.051 2.00e-02 2.50e+03 pdb=" CA MET D 320 " 0.014 2.00e-02 2.50e+03 pdb=" H MET D 320 " 0.022 2.00e-02 2.50e+03 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 637 2.14 - 2.76: 57834 2.76 - 3.37: 83456 3.37 - 3.99: 100986 3.99 - 4.60: 161131 Nonbonded interactions: 404044 Sorted by model distance: nonbonded pdb=" HG3 LYS A 743 " pdb=" HE2 PHE B 316 " model vdw 1.528 2.270 nonbonded pdb=" HG3 LYS B 743 " pdb=" HE2 PHE C 316 " model vdw 1.531 2.270 nonbonded pdb=" HE2 PHE A 316 " pdb=" HG3 LYS D 743 " model vdw 1.534 2.270 nonbonded pdb=" HE2 PHE D 316 " pdb=" HG3 LYS C 743 " model vdw 1.535 2.270 nonbonded pdb=" O LEU D 563 " pdb=" HG1 THR D 566 " model vdw 1.661 2.450 ... (remaining 404039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 1 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 170 through 750)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.610 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 17692 Z= 0.430 Angle : 0.873 8.962 24240 Z= 0.519 Chirality : 0.046 0.155 3004 Planarity : 0.005 0.045 3024 Dihedral : 8.411 43.917 5404 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.15), residues: 2412 helix: -0.89 (0.11), residues: 1668 sheet: -2.72 (0.55), residues: 68 loop : -2.62 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 375 TYR 0.022 0.003 TYR C 460 PHE 0.030 0.003 PHE A 526 TRP 0.028 0.003 TRP D 493 HIS 0.006 0.002 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00928 (17692) covalent geometry : angle 0.87347 (24240) hydrogen bonds : bond 0.15193 ( 1212) hydrogen bonds : angle 6.17765 ( 3576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 691 ILE cc_start: 0.9369 (mt) cc_final: 0.9168 (tp) REVERT: D 691 ILE cc_start: 0.9368 (mt) cc_final: 0.9163 (tp) REVERT: C 691 ILE cc_start: 0.9368 (mt) cc_final: 0.9167 (tp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2837 time to fit residues: 143.4264 Evaluate side-chains 219 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.108150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092637 restraints weight = 142864.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096272 restraints weight = 64790.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098674 restraints weight = 37439.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099926 restraints weight = 25134.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101103 restraints weight = 19614.387| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17692 Z= 0.185 Angle : 0.543 6.228 24240 Z= 0.304 Chirality : 0.034 0.128 3004 Planarity : 0.004 0.036 3024 Dihedral : 4.308 23.296 2640 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.30 % Allowed : 3.11 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2412 helix: 0.74 (0.12), residues: 1676 sheet: -2.25 (0.57), residues: 64 loop : -2.55 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 375 TYR 0.017 0.002 TYR D 359 PHE 0.017 0.001 PHE B 316 TRP 0.011 0.001 TRP A 559 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00373 (17692) covalent geometry : angle 0.54298 (24240) hydrogen bonds : bond 0.04352 ( 1212) hydrogen bonds : angle 4.75785 ( 3576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.8236 (tmm) cc_final: 0.8016 (tmm) REVERT: B 555 MET cc_start: 0.8246 (tmm) cc_final: 0.8017 (tmm) REVERT: B 691 ILE cc_start: 0.9386 (mt) cc_final: 0.9149 (tp) REVERT: D 555 MET cc_start: 0.8255 (tmm) cc_final: 0.8050 (tmm) REVERT: D 691 ILE cc_start: 0.9381 (mt) cc_final: 0.9154 (tp) REVERT: C 555 MET cc_start: 0.8265 (tmm) cc_final: 0.8023 (tmm) REVERT: C 691 ILE cc_start: 0.9389 (mt) cc_final: 0.9149 (tp) outliers start: 4 outliers final: 4 residues processed: 283 average time/residue: 0.2067 time to fit residues: 99.4901 Evaluate side-chains 221 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 166 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 301 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 301 HIS B 671 ASN D 273 ASN D 301 HIS D 671 ASN C 273 ASN C 301 HIS C 671 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089793 restraints weight = 144217.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093370 restraints weight = 65936.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095701 restraints weight = 38256.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097189 restraints weight = 25811.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098120 restraints weight = 19583.729| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17692 Z= 0.217 Angle : 0.543 4.796 24240 Z= 0.304 Chirality : 0.035 0.131 3004 Planarity : 0.003 0.032 3024 Dihedral : 4.088 23.818 2640 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2412 helix: 1.30 (0.13), residues: 1668 sheet: -1.06 (0.64), residues: 56 loop : -2.24 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.018 0.002 TYR D 448 PHE 0.013 0.002 PHE A 259 TRP 0.010 0.002 TRP A 559 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00460 (17692) covalent geometry : angle 0.54266 (24240) hydrogen bonds : bond 0.04219 ( 1212) hydrogen bonds : angle 4.61262 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 691 ILE cc_start: 0.9339 (mt) cc_final: 0.9083 (tp) REVERT: B 701 LEU cc_start: 0.9226 (tp) cc_final: 0.8867 (tt) REVERT: D 691 ILE cc_start: 0.9347 (mt) cc_final: 0.9096 (tp) REVERT: C 691 ILE cc_start: 0.9337 (mt) cc_final: 0.9082 (tp) REVERT: C 701 LEU cc_start: 0.9232 (tp) cc_final: 0.8871 (tt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2189 time to fit residues: 96.8812 Evaluate side-chains 227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087453 restraints weight = 144674.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.090950 restraints weight = 65994.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093262 restraints weight = 38213.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.094457 restraints weight = 25945.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095563 restraints weight = 20477.497| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17692 Z= 0.242 Angle : 0.580 5.448 24240 Z= 0.322 Chirality : 0.035 0.136 3004 Planarity : 0.004 0.029 3024 Dihedral : 4.169 21.728 2640 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2412 helix: 1.35 (0.13), residues: 1672 sheet: -0.73 (0.68), residues: 56 loop : -2.21 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 375 TYR 0.018 0.002 TYR A 208 PHE 0.015 0.002 PHE B 259 TRP 0.011 0.002 TRP B 559 HIS 0.005 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00506 (17692) covalent geometry : angle 0.58047 (24240) hydrogen bonds : bond 0.04108 ( 1212) hydrogen bonds : angle 4.67152 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TRP cc_start: 0.6950 (t60) cc_final: 0.6716 (t-100) REVERT: A 653 LEU cc_start: 0.9037 (tp) cc_final: 0.8759 (mm) REVERT: A 692 TRP cc_start: 0.8509 (t60) cc_final: 0.8122 (t60) REVERT: B 380 TRP cc_start: 0.6952 (t60) cc_final: 0.6724 (t-100) REVERT: B 691 ILE cc_start: 0.9353 (mt) cc_final: 0.9121 (tp) REVERT: B 692 TRP cc_start: 0.8509 (t60) cc_final: 0.8116 (t60) REVERT: B 701 LEU cc_start: 0.9298 (tp) cc_final: 0.8962 (tt) REVERT: D 380 TRP cc_start: 0.6954 (t60) cc_final: 0.6724 (t-100) REVERT: D 653 LEU cc_start: 0.9041 (tp) cc_final: 0.8765 (mm) REVERT: D 691 ILE cc_start: 0.9360 (mt) cc_final: 0.9129 (tp) REVERT: D 692 TRP cc_start: 0.8506 (t60) cc_final: 0.8108 (t60) REVERT: C 380 TRP cc_start: 0.7020 (t60) cc_final: 0.6804 (t-100) REVERT: C 653 LEU cc_start: 0.9036 (tp) cc_final: 0.8761 (mm) REVERT: C 691 ILE cc_start: 0.9351 (mt) cc_final: 0.9121 (tp) REVERT: C 692 TRP cc_start: 0.8499 (t60) cc_final: 0.8102 (t60) REVERT: C 701 LEU cc_start: 0.9304 (tp) cc_final: 0.8966 (tt) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2132 time to fit residues: 96.3203 Evaluate side-chains 216 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 60 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 187 optimal weight: 30.0000 chunk 63 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085647 restraints weight = 146218.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089042 restraints weight = 66842.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091330 restraints weight = 38896.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092801 restraints weight = 26270.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093661 restraints weight = 19906.251| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17692 Z= 0.313 Angle : 0.653 5.810 24240 Z= 0.366 Chirality : 0.037 0.142 3004 Planarity : 0.005 0.048 3024 Dihedral : 4.523 29.370 2640 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2412 helix: 0.96 (0.13), residues: 1652 sheet: -1.06 (0.65), residues: 56 loop : -2.01 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 295 TYR 0.021 0.003 TYR D 208 PHE 0.016 0.002 PHE B 259 TRP 0.010 0.002 TRP A 559 HIS 0.006 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00661 (17692) covalent geometry : angle 0.65263 (24240) hydrogen bonds : bond 0.04510 ( 1212) hydrogen bonds : angle 5.01482 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 653 LEU cc_start: 0.9153 (tp) cc_final: 0.8791 (mm) REVERT: B 653 LEU cc_start: 0.9116 (tp) cc_final: 0.8797 (mm) REVERT: B 672 MET cc_start: 0.9136 (tmm) cc_final: 0.8914 (tmm) REVERT: B 691 ILE cc_start: 0.9367 (mt) cc_final: 0.9154 (tp) REVERT: B 701 LEU cc_start: 0.9349 (tp) cc_final: 0.8982 (tt) REVERT: D 653 LEU cc_start: 0.9157 (tp) cc_final: 0.8796 (mm) REVERT: D 691 ILE cc_start: 0.9366 (mt) cc_final: 0.9155 (tp) REVERT: C 653 LEU cc_start: 0.9145 (tp) cc_final: 0.8788 (mm) REVERT: C 672 MET cc_start: 0.9141 (tmm) cc_final: 0.8919 (tmm) REVERT: C 691 ILE cc_start: 0.9362 (mt) cc_final: 0.9152 (tp) REVERT: C 701 LEU cc_start: 0.9355 (tp) cc_final: 0.8984 (tt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2067 time to fit residues: 85.6742 Evaluate side-chains 211 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 75 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089071 restraints weight = 143497.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092683 restraints weight = 64065.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094978 restraints weight = 36375.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096472 restraints weight = 24471.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097461 restraints weight = 18424.555| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17692 Z= 0.163 Angle : 0.496 4.674 24240 Z= 0.280 Chirality : 0.034 0.131 3004 Planarity : 0.003 0.028 3024 Dihedral : 4.053 24.848 2640 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2412 helix: 1.48 (0.13), residues: 1672 sheet: -1.67 (0.60), residues: 64 loop : -2.07 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 375 TYR 0.015 0.002 TYR A 448 PHE 0.020 0.001 PHE A 447 TRP 0.010 0.001 TRP A 559 HIS 0.002 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00340 (17692) covalent geometry : angle 0.49644 (24240) hydrogen bonds : bond 0.03874 ( 1212) hydrogen bonds : angle 4.39504 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.9339 (tt) cc_final: 0.9129 (tt) REVERT: A 653 LEU cc_start: 0.9093 (tp) cc_final: 0.8755 (mm) REVERT: A 692 TRP cc_start: 0.8604 (t60) cc_final: 0.8217 (t60) REVERT: B 268 LEU cc_start: 0.9335 (tt) cc_final: 0.9132 (tt) REVERT: B 653 LEU cc_start: 0.9032 (tp) cc_final: 0.8712 (mm) REVERT: B 691 ILE cc_start: 0.9318 (mt) cc_final: 0.9103 (tp) REVERT: B 701 LEU cc_start: 0.9307 (tp) cc_final: 0.9084 (tt) REVERT: D 268 LEU cc_start: 0.9341 (tt) cc_final: 0.9131 (tt) REVERT: D 653 LEU cc_start: 0.9073 (tp) cc_final: 0.8724 (mm) REVERT: D 691 ILE cc_start: 0.9319 (mt) cc_final: 0.9110 (tp) REVERT: C 268 LEU cc_start: 0.9336 (tt) cc_final: 0.9134 (tt) REVERT: C 653 LEU cc_start: 0.9064 (tp) cc_final: 0.8719 (mm) REVERT: C 701 LEU cc_start: 0.9313 (tp) cc_final: 0.9085 (tt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2061 time to fit residues: 99.7604 Evaluate side-chains 227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 74 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088108 restraints weight = 145818.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091588 restraints weight = 66161.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093905 restraints weight = 38346.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.095405 restraints weight = 25955.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096193 restraints weight = 19597.116| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17692 Z= 0.174 Angle : 0.498 4.919 24240 Z= 0.280 Chirality : 0.034 0.131 3004 Planarity : 0.003 0.025 3024 Dihedral : 3.887 23.278 2640 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2412 helix: 1.71 (0.13), residues: 1684 sheet: -1.62 (0.62), residues: 64 loop : -1.99 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.017 0.002 TYR C 448 PHE 0.011 0.001 PHE A 259 TRP 0.009 0.001 TRP D 559 HIS 0.003 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00363 (17692) covalent geometry : angle 0.49832 (24240) hydrogen bonds : bond 0.03686 ( 1212) hydrogen bonds : angle 4.31007 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 653 LEU cc_start: 0.9128 (tp) cc_final: 0.8781 (mm) REVERT: B 701 LEU cc_start: 0.9322 (tp) cc_final: 0.9093 (tt) REVERT: C 701 LEU cc_start: 0.9326 (tp) cc_final: 0.9088 (tt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2073 time to fit residues: 97.4708 Evaluate side-chains 227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 165 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 671 ASN D 273 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088641 restraints weight = 146866.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092311 restraints weight = 65084.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094706 restraints weight = 37094.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096254 restraints weight = 24861.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097210 restraints weight = 18687.378| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17692 Z= 0.169 Angle : 0.496 5.185 24240 Z= 0.276 Chirality : 0.034 0.128 3004 Planarity : 0.003 0.025 3024 Dihedral : 3.804 22.394 2640 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2412 helix: 1.80 (0.13), residues: 1680 sheet: -1.26 (0.62), residues: 68 loop : -2.05 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 375 TYR 0.012 0.002 TYR D 390 PHE 0.011 0.001 PHE A 259 TRP 0.007 0.001 TRP D 559 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00352 (17692) covalent geometry : angle 0.49635 (24240) hydrogen bonds : bond 0.03599 ( 1212) hydrogen bonds : angle 4.23659 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 ASP cc_start: 0.8804 (p0) cc_final: 0.7598 (p0) REVERT: B 701 LEU cc_start: 0.9314 (tp) cc_final: 0.9075 (tt) REVERT: D 293 ASP cc_start: 0.8795 (p0) cc_final: 0.7606 (p0) REVERT: C 293 ASP cc_start: 0.8803 (p0) cc_final: 0.7593 (p0) REVERT: C 701 LEU cc_start: 0.9303 (tp) cc_final: 0.9051 (tt) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1974 time to fit residues: 89.9505 Evaluate side-chains 228 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 108 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088874 restraints weight = 144972.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092531 restraints weight = 62824.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094878 restraints weight = 35220.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096142 restraints weight = 23405.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097234 restraints weight = 18136.441| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17692 Z= 0.156 Angle : 0.487 5.216 24240 Z= 0.269 Chirality : 0.034 0.125 3004 Planarity : 0.003 0.025 3024 Dihedral : 3.714 21.910 2640 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2412 helix: 1.93 (0.13), residues: 1680 sheet: -1.32 (0.61), residues: 68 loop : -2.01 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.012 0.002 TYR B 390 PHE 0.011 0.001 PHE A 259 TRP 0.006 0.001 TRP A 559 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00324 (17692) covalent geometry : angle 0.48680 (24240) hydrogen bonds : bond 0.03491 ( 1212) hydrogen bonds : angle 4.14646 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8755 (p0) cc_final: 0.7576 (p0) REVERT: B 293 ASP cc_start: 0.8786 (p0) cc_final: 0.7578 (p0) REVERT: B 701 LEU cc_start: 0.9297 (tp) cc_final: 0.9060 (tt) REVERT: D 293 ASP cc_start: 0.8782 (p0) cc_final: 0.7586 (p0) REVERT: C 293 ASP cc_start: 0.8786 (p0) cc_final: 0.7576 (p0) REVERT: C 701 LEU cc_start: 0.9304 (tp) cc_final: 0.9061 (tt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2023 time to fit residues: 94.2944 Evaluate side-chains 228 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 210 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 671 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089643 restraints weight = 144730.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093363 restraints weight = 62564.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095738 restraints weight = 35054.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097272 restraints weight = 23313.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.098327 restraints weight = 17418.528| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17692 Z= 0.124 Angle : 0.460 5.366 24240 Z= 0.254 Chirality : 0.033 0.126 3004 Planarity : 0.003 0.025 3024 Dihedral : 3.660 27.897 2640 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 2412 helix: 2.13 (0.13), residues: 1680 sheet: -1.31 (0.61), residues: 68 loop : -1.86 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.017 0.001 TYR D 448 PHE 0.012 0.001 PHE A 592 TRP 0.006 0.001 TRP B 559 HIS 0.002 0.000 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00256 (17692) covalent geometry : angle 0.45990 (24240) hydrogen bonds : bond 0.03325 ( 1212) hydrogen bonds : angle 3.96096 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue VAL 136 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue ALA 169 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue THR 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 320 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue LEU 326 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue SER 498 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue SER 536 is missing expected H atoms. Skipping. Residue VAL 537 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue VAL 577 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 579 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8710 (p0) cc_final: 0.7641 (p0) REVERT: B 293 ASP cc_start: 0.8731 (p0) cc_final: 0.7568 (p0) REVERT: B 665 THR cc_start: 0.8495 (m) cc_final: 0.8270 (m) REVERT: B 701 LEU cc_start: 0.9278 (tp) cc_final: 0.8907 (tt) REVERT: D 293 ASP cc_start: 0.8734 (p0) cc_final: 0.7578 (p0) REVERT: D 665 THR cc_start: 0.8525 (m) cc_final: 0.8298 (m) REVERT: C 293 ASP cc_start: 0.8736 (p0) cc_final: 0.7565 (p0) REVERT: C 665 THR cc_start: 0.8504 (m) cc_final: 0.8277 (m) REVERT: C 701 LEU cc_start: 0.9283 (tp) cc_final: 0.8906 (tt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2037 time to fit residues: 94.8145 Evaluate side-chains 228 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 26 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 212 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 671 ASN B 273 ASN B 671 ASN D 671 ASN C 273 ASN C 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089116 restraints weight = 146513.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092845 restraints weight = 65010.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095228 restraints weight = 37367.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096827 restraints weight = 25371.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097901 restraints weight = 19143.343| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17692 Z= 0.161 Angle : 0.485 5.100 24240 Z= 0.269 Chirality : 0.034 0.123 3004 Planarity : 0.003 0.024 3024 Dihedral : 3.661 27.249 2640 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2412 helix: 2.16 (0.13), residues: 1660 sheet: -1.34 (0.60), residues: 68 loop : -1.66 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 375 TYR 0.011 0.002 TYR D 390 PHE 0.014 0.001 PHE A 436 TRP 0.006 0.001 TRP D 739 HIS 0.002 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00335 (17692) covalent geometry : angle 0.48505 (24240) hydrogen bonds : bond 0.03443 ( 1212) hydrogen bonds : angle 4.06550 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4307.64 seconds wall clock time: 74 minutes 20.00 seconds (4460.00 seconds total)