Starting phenix.real_space_refine on Fri Mar 6 19:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot5_20194/03_2026/6ot5_20194.map" } resolution = 3.6 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= 0.008 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: 6 Type Number sf(0) Gaussians S 80 5.16 5 B 4 2.79 5 C 11664 2.51 5 N 3036 2.21 5 O 3016 1.98 5 H 15620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 33420 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 8338 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 611} Chain breaks: 4 Unresolved non-hydrogen bonds: 649 Unresolved non-hydrogen angles: 809 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'UNK:plan-1': 12, 'GLU:plan': 38, 'GLN:plan1': 7, 'ARG:plan': 14, 'ASP:plan': 14, 'PHE:plan': 6, 'ASN:plan1': 11, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 399 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 10.88, per 1000 atoms: 0.33 Number of scatterers: 33420 At special positions: 0 Unit cell: (141.48, 141.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 O 3016 8.00 N 3036 7.00 C 11664 6.00 B 4 5.00 H 15620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.04 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 Atom "HETATM33403 O14 FZ4 C1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33420 O14 FZ4 D1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33369 O14 FZ4 A1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM33386 O14 FZ4 B1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.3 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: 4768 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 70.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 111 through 130 removed outlier: 3.914A pdb=" N LYS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 149 removed outlier: 4.070A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) 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: 3.820A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.685A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.561A pdb=" N ALA A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.535A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.589A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.522A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.897A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.883A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.511A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.605A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 585 through 609 removed outlier: 4.422A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.638A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 667 removed outlier: 3.759A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 707 removed outlier: 4.185A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.644A pdb=" N ARG A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 removed outlier: 3.610A pdb=" N TRP A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.913A pdb=" N LYS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 removed outlier: 4.071A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) 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: 3.820A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.685A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.561A pdb=" N ALA B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.536A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.589A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.522A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.897A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.883A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.511A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.606A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 609 removed outlier: 4.422A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 636 removed outlier: 3.638A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.759A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 707 removed outlier: 4.185A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.644A pdb=" N ARG B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 removed outlier: 3.610A pdb=" N TRP B 742 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 130 removed outlier: 3.914A pdb=" N LYS C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 removed outlier: 4.071A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) 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: 3.820A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.685A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.561A pdb=" N ALA C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.536A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.589A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.522A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.897A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.883A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.511A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.606A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 583 Processing helix chain 'C' and resid 585 through 609 removed outlier: 4.422A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.638A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 667 removed outlier: 3.759A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 707 removed outlier: 4.185A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.644A pdb=" N ARG C 712 " --> pdb=" O PRO C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 750 removed outlier: 3.610A pdb=" N TRP C 742 " --> pdb=" O LYS C 738 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.914A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 removed outlier: 4.071A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) 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: 3.820A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.685A pdb=" N GLY D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.561A pdb=" N ALA D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.536A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 removed outlier: 3.589A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.522A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.897A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.883A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.511A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.606A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 583 Processing helix chain 'D' and resid 585 through 609 removed outlier: 4.422A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 636 removed outlier: 3.639A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 667 removed outlier: 3.759A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 707 removed outlier: 4.185A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.644A pdb=" N ARG D 712 " --> pdb=" O PRO D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 750 removed outlier: 3.610A pdb=" N TRP D 742 " --> pdb=" O LYS D 738 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 3.688A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.224A 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: 3.688A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 3.688A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 3.688A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3360 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: 7.47 Time building geometry restraints manager: 4.35 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: 15608 1.02 - 1.22: 12 1.22 - 1.43: 7696 1.43 - 1.63: 10348 1.63 - 1.83: 128 Bond restraints: 33792 Sorted by residual: bond pdb=" ND2 ASN C 314 " pdb="HD21 ASN C 314 " 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 D 314 " pdb="HD21 ASN D 314 " 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 314 " pdb="HD21 ASN B 314 " 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 D 314 " pdb="HD22 ASN D 314 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN B 314 " pdb="HD22 ASN B 314 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 57785 1.78 - 3.57: 2358 3.57 - 5.35: 177 5.35 - 7.14: 32 7.14 - 8.92: 12 Bond angle restraints: 60364 Sorted by residual: angle pdb=" N MET A 351 " pdb=" CA MET A 351 " pdb=" C MET A 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.64e+01 angle pdb=" N MET C 351 " pdb=" CA MET C 351 " pdb=" C MET C 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N MET B 351 " pdb=" CA MET B 351 " pdb=" C MET B 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N MET D 351 " pdb=" CA MET D 351 " pdb=" C MET D 351 " ideal model delta sigma weight residual 110.50 104.80 5.70 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N PHE A 748 " pdb=" CA PHE A 748 " pdb=" C PHE A 748 " ideal model delta sigma weight residual 111.28 114.98 -3.70 1.09e+00 8.42e-01 1.15e+01 ... (remaining 60359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 16021 31.38 - 62.75: 295 62.75 - 94.12: 8 94.12 - 125.50: 0 125.50 - 156.87: 4 Dihedral angle restraints: 16328 sinusoidal: 7632 harmonic: 8696 Sorted by residual: dihedral pdb=" CA VAL A 684 " pdb=" C VAL A 684 " pdb=" N SER A 685 " pdb=" CA SER A 685 " ideal model delta harmonic sigma weight residual -180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL D 684 " pdb=" C VAL D 684 " pdb=" N SER D 685 " pdb=" CA SER D 685 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA VAL B 684 " pdb=" C VAL B 684 " pdb=" N SER B 685 " pdb=" CA SER B 685 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 16325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1944 0.039 - 0.078: 777 0.078 - 0.117: 243 0.117 - 0.155: 48 0.155 - 0.194: 12 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CG LEU B 425 " pdb=" CB LEU B 425 " pdb=" CD1 LEU B 425 " pdb=" CD2 LEU B 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU C 425 " pdb=" CB LEU C 425 " pdb=" CD1 LEU C 425 " pdb=" CD2 LEU C 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CG LEU D 425 " pdb=" CB LEU D 425 " pdb=" CD1 LEU D 425 " pdb=" CD2 LEU D 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 3021 not shown) Planarity restraints: 5468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA B 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA B 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA B 354 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA C 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA C 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA C 354 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" N ALA D 354 " -0.036 2.00e-02 2.50e+03 pdb=" CA ALA D 354 " 0.009 2.00e-02 2.50e+03 pdb=" H ALA D 354 " 0.016 2.00e-02 2.50e+03 ... (remaining 5465 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 216 2.08 - 2.71: 51499 2.71 - 3.34: 87143 3.34 - 3.97: 104859 3.97 - 4.60: 171280 Nonbonded interactions: 414997 Sorted by model distance: nonbonded pdb="HD11 LEU B 347 " pdb=" HE3 MET B 351 " model vdw 1.448 2.440 nonbonded pdb="HD11 LEU D 347 " pdb=" HE3 MET D 351 " model vdw 1.448 2.440 nonbonded pdb="HD11 LEU C 347 " pdb=" HE3 MET C 351 " model vdw 1.448 2.440 nonbonded pdb="HD11 LEU A 347 " pdb=" HE3 MET A 351 " model vdw 1.449 2.440 nonbonded pdb=" HH TYR B 321 " pdb=" OE2 GLU B 334 " model vdw 1.644 2.450 ... (remaining 414992 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.780 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: 0.190 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.010 0.193 18180 Z= 0.473 Angle : 0.858 8.923 24832 Z= 0.461 Chirality : 0.047 0.194 3024 Planarity : 0.005 0.043 3088 Dihedral : 10.202 156.875 5728 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -2.73 (0.15), residues: 2412 helix: -1.57 (0.11), residues: 1536 sheet: -2.03 (0.52), residues: 72 loop : -1.94 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 375 TYR 0.030 0.003 TYR D 409 PHE 0.025 0.003 PHE B 449 TRP 0.020 0.002 TRP A 380 HIS 0.010 0.003 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00936 (18172) covalent geometry : angle 0.85632 (24824) SS BOND : bond 0.00629 ( 4) SS BOND : angle 3.47955 ( 8) hydrogen bonds : bond 0.16031 ( 1152) hydrogen bonds : angle 6.26563 ( 3360) Misc. bond : bond 0.19318 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.3105 time to fit residues: 168.8554 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 : 0.578 ------------------------------------------------------------------------------- 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: 0.5980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 735 ASN ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 580 GLN B 585 HIS ** C 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 580 GLN C 585 HIS ** D 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 580 GLN D 585 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.175020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151996 restraints weight = 62146.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.155600 restraints weight = 39391.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.158099 restraints weight = 28220.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.159756 restraints weight = 22248.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.160560 restraints weight = 18824.480| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18180 Z= 0.217 Angle : 0.611 5.160 24832 Z= 0.338 Chirality : 0.037 0.122 3024 Planarity : 0.004 0.057 3088 Dihedral : 7.691 129.038 2660 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.03 % Allowed : 8.61 % Favored : 90.36 % 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: -1.15 (0.16), residues: 2412 helix: -0.18 (0.12), residues: 1604 sheet: -2.82 (0.47), residues: 96 loop : -1.54 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 226 TYR 0.022 0.002 TYR B 208 PHE 0.016 0.002 PHE A 259 TRP 0.013 0.001 TRP C 521 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00497 (18172) covalent geometry : angle 0.60938 (24824) SS BOND : bond 0.00805 ( 4) SS BOND : angle 2.70691 ( 8) hydrogen bonds : bond 0.05543 ( 1152) hydrogen bonds : angle 4.76722 ( 3360) Misc. bond : bond 0.00110 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 258 average time/residue: 0.2345 time to fit residues: 98.7328 Evaluate side-chains 226 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 721 CYS Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 721 CYS Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 221 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 580 GLN A 585 HIS ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 314 ASN B 580 GLN B 735 ASN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 314 ASN C 580 GLN C 735 ASN ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 314 ASN D 580 GLN D 735 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146345 restraints weight = 63566.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149753 restraints weight = 40761.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152036 restraints weight = 29621.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.153719 restraints weight = 23748.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154502 restraints weight = 20122.008| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18180 Z= 0.222 Angle : 0.576 5.050 24832 Z= 0.322 Chirality : 0.036 0.120 3024 Planarity : 0.004 0.032 3088 Dihedral : 6.330 79.482 2660 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.31 % Allowed : 9.57 % Favored : 89.12 % 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: -0.52 (0.17), residues: 2412 helix: 0.35 (0.13), residues: 1616 sheet: -2.31 (0.49), residues: 96 loop : -1.52 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 416 TYR 0.021 0.002 TYR C 390 PHE 0.018 0.002 PHE B 316 TRP 0.019 0.001 TRP D 380 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00520 (18172) covalent geometry : angle 0.57382 (24824) SS BOND : bond 0.00177 ( 4) SS BOND : angle 3.04495 ( 8) hydrogen bonds : bond 0.05373 ( 1152) hydrogen bonds : angle 4.51457 ( 3360) Misc. bond : bond 0.00064 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.822 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: A 572 MET cc_start: 0.6534 (mmm) cc_final: 0.6315 (mmt) REVERT: B 572 MET cc_start: 0.6542 (mmm) cc_final: 0.6329 (mmt) REVERT: C 572 MET cc_start: 0.6551 (mmm) cc_final: 0.6337 (mmt) REVERT: D 572 MET cc_start: 0.6546 (mmm) cc_final: 0.6325 (mmt) outliers start: 19 outliers final: 16 residues processed: 242 average time/residue: 0.2275 time to fit residues: 90.1269 Evaluate side-chains 220 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 224 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 273 ASN A 580 GLN ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 273 ASN B 580 GLN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 273 ASN C 580 GLN ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN D 273 ASN D 580 GLN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.171809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149224 restraints weight = 62499.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152662 restraints weight = 39910.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154631 restraints weight = 29036.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156181 restraints weight = 23229.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157615 restraints weight = 19708.643| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18180 Z= 0.139 Angle : 0.484 4.958 24832 Z= 0.268 Chirality : 0.033 0.122 3024 Planarity : 0.003 0.028 3088 Dihedral : 4.925 58.274 2660 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.38 % Allowed : 11.43 % Favored : 87.19 % 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: 0.19 (0.17), residues: 2412 helix: 0.96 (0.13), residues: 1628 sheet: -0.58 (0.66), residues: 64 loop : -1.69 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 416 TYR 0.013 0.002 TYR A 208 PHE 0.014 0.001 PHE A 193 TRP 0.018 0.001 TRP D 380 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00308 (18172) covalent geometry : angle 0.48239 (24824) SS BOND : bond 0.00106 ( 4) SS BOND : angle 2.28212 ( 8) hydrogen bonds : bond 0.04445 ( 1152) hydrogen bonds : angle 4.10956 ( 3360) Misc. bond : bond 0.00113 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 223 average time/residue: 0.2231 time to fit residues: 82.1934 Evaluate side-chains 213 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 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 580 GLN ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147935 restraints weight = 63631.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150401 restraints weight = 40674.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150741 restraints weight = 32074.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150938 restraints weight = 28689.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151150 restraints weight = 28521.924| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18180 Z= 0.163 Angle : 0.495 5.441 24832 Z= 0.275 Chirality : 0.034 0.121 3024 Planarity : 0.003 0.028 3088 Dihedral : 4.841 58.025 2660 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.45 % Allowed : 12.88 % Favored : 85.67 % 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: 0.44 (0.18), residues: 2412 helix: 1.17 (0.13), residues: 1624 sheet: -0.32 (0.71), residues: 64 loop : -1.66 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.014 0.002 TYR A 208 PHE 0.014 0.001 PHE D 193 TRP 0.023 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00376 (18172) covalent geometry : angle 0.49369 (24824) SS BOND : bond 0.00054 ( 4) SS BOND : angle 2.30474 ( 8) hydrogen bonds : bond 0.04474 ( 1152) hydrogen bonds : angle 4.04235 ( 3360) Misc. bond : bond 0.00034 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.846 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: A 208 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7376 (t80) REVERT: B 208 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 431 MET cc_start: 0.5943 (mtp) cc_final: 0.5701 (mtt) REVERT: C 208 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7383 (t80) REVERT: C 431 MET cc_start: 0.5896 (mtp) cc_final: 0.5664 (mtt) REVERT: D 208 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7385 (t80) REVERT: D 431 MET cc_start: 0.5917 (mtp) cc_final: 0.5680 (mtt) outliers start: 21 outliers final: 13 residues processed: 214 average time/residue: 0.2256 time to fit residues: 78.7527 Evaluate side-chains 211 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148273 restraints weight = 62943.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151706 restraints weight = 40822.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.153604 restraints weight = 29711.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.155433 restraints weight = 23938.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.156256 restraints weight = 20387.688| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18180 Z= 0.133 Angle : 0.459 5.431 24832 Z= 0.254 Chirality : 0.033 0.120 3024 Planarity : 0.003 0.026 3088 Dihedral : 4.640 54.875 2660 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.45 % Allowed : 13.50 % Favored : 85.06 % 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: 0.74 (0.18), residues: 2412 helix: 1.40 (0.13), residues: 1644 sheet: -0.04 (0.74), residues: 64 loop : -1.64 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 416 TYR 0.014 0.002 TYR B 208 PHE 0.015 0.001 PHE A 193 TRP 0.020 0.001 TRP C 380 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00297 (18172) covalent geometry : angle 0.45705 (24824) SS BOND : bond 0.00129 ( 4) SS BOND : angle 2.10906 ( 8) hydrogen bonds : bond 0.04102 ( 1152) hydrogen bonds : angle 3.87406 ( 3360) Misc. bond : bond 0.00031 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.765 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: A 208 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 208 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 208 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7119 (t80) REVERT: D 208 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7122 (t80) outliers start: 21 outliers final: 8 residues processed: 221 average time/residue: 0.2198 time to fit residues: 81.0832 Evaluate side-chains 212 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143327 restraints weight = 64113.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146306 restraints weight = 42154.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.148828 restraints weight = 31302.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150132 restraints weight = 25245.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151420 restraints weight = 21664.614| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18180 Z= 0.209 Angle : 0.539 5.131 24832 Z= 0.299 Chirality : 0.035 0.119 3024 Planarity : 0.003 0.031 3088 Dihedral : 4.986 56.816 2660 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.65 % Allowed : 13.84 % Favored : 84.50 % 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: 0.62 (0.18), residues: 2412 helix: 1.41 (0.13), residues: 1584 sheet: -0.89 (0.58), residues: 96 loop : -1.64 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.019 0.002 TYR A 409 PHE 0.013 0.002 PHE A 193 TRP 0.016 0.001 TRP C 380 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00490 (18172) covalent geometry : angle 0.53761 (24824) SS BOND : bond 0.00087 ( 4) SS BOND : angle 2.33561 ( 8) hydrogen bonds : bond 0.04886 ( 1152) hydrogen bonds : angle 4.10499 ( 3360) Misc. bond : bond 0.00008 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.884 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: A 208 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.6780 (t80) REVERT: B 208 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.6802 (t80) REVERT: C 208 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.6777 (t80) REVERT: D 208 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6780 (t80) outliers start: 24 outliers final: 16 residues processed: 232 average time/residue: 0.2191 time to fit residues: 84.9908 Evaluate side-chains 201 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 170 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.170334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148865 restraints weight = 62778.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151864 restraints weight = 41042.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153738 restraints weight = 30297.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155437 restraints weight = 24468.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156275 restraints weight = 20915.690| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18180 Z= 0.111 Angle : 0.449 4.804 24832 Z= 0.247 Chirality : 0.032 0.123 3024 Planarity : 0.003 0.026 3088 Dihedral : 4.578 53.020 2660 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.45 % Allowed : 14.05 % Favored : 84.50 % 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: 0.99 (0.18), residues: 2412 helix: 1.62 (0.13), residues: 1644 sheet: 0.12 (0.77), residues: 64 loop : -1.66 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 416 TYR 0.012 0.001 TYR A 208 PHE 0.016 0.001 PHE B 193 TRP 0.021 0.001 TRP C 380 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00239 (18172) covalent geometry : angle 0.44783 (24824) SS BOND : bond 0.00204 ( 4) SS BOND : angle 1.99314 ( 8) hydrogen bonds : bond 0.03940 ( 1152) hydrogen bonds : angle 3.80361 ( 3360) Misc. bond : bond 0.00052 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.923 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: A 208 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.6885 (t80) REVERT: B 208 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.6849 (t80) REVERT: C 208 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6884 (t80) REVERT: D 208 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.6888 (t80) outliers start: 21 outliers final: 6 residues processed: 223 average time/residue: 0.2222 time to fit residues: 82.4889 Evaluate side-chains 199 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.145968 restraints weight = 63074.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149304 restraints weight = 40866.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151237 restraints weight = 29970.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152748 restraints weight = 24118.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154114 restraints weight = 20576.597| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18180 Z= 0.137 Angle : 0.467 4.771 24832 Z= 0.257 Chirality : 0.033 0.123 3024 Planarity : 0.003 0.026 3088 Dihedral : 4.552 51.341 2660 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.38 % Allowed : 14.53 % Favored : 84.09 % 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: 1.08 (0.18), residues: 2412 helix: 1.69 (0.13), residues: 1644 sheet: 0.30 (0.78), residues: 64 loop : -1.64 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 416 TYR 0.013 0.002 TYR C 409 PHE 0.015 0.001 PHE A 193 TRP 0.019 0.001 TRP C 380 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00310 (18172) covalent geometry : angle 0.46549 (24824) SS BOND : bond 0.00121 ( 4) SS BOND : angle 2.12878 ( 8) hydrogen bonds : bond 0.04103 ( 1152) hydrogen bonds : angle 3.80866 ( 3360) Misc. bond : bond 0.00029 ( 4) *********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.854 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: A 208 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.6674 (t80) REVERT: B 208 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.6735 (t80) REVERT: C 208 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6686 (t80) REVERT: D 208 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6690 (t80) outliers start: 20 outliers final: 11 residues processed: 202 average time/residue: 0.2243 time to fit residues: 74.6715 Evaluate side-chains 198 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 239 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146290 restraints weight = 63335.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149616 restraints weight = 40875.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.151530 restraints weight = 29980.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153072 restraints weight = 24198.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.154470 restraints weight = 20690.494| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 18180 Z= 0.247 Angle : 0.814 59.194 24832 Z= 0.495 Chirality : 0.034 0.263 3024 Planarity : 0.003 0.049 3088 Dihedral : 4.555 51.352 2660 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.10 % Allowed : 14.46 % Favored : 84.44 % Cbeta Deviations : 0.08 % 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: 1.07 (0.18), residues: 2412 helix: 1.68 (0.13), residues: 1644 sheet: 0.31 (0.78), residues: 64 loop : -1.65 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 416 TYR 0.013 0.002 TYR B 208 PHE 0.014 0.001 PHE A 193 TRP 0.017 0.001 TRP C 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00508 (18172) covalent geometry : angle 0.81287 (24824) SS BOND : bond 0.00064 ( 4) SS BOND : angle 2.11146 ( 8) hydrogen bonds : bond 0.04135 ( 1152) hydrogen bonds : angle 3.81198 ( 3360) Misc. bond : bond 0.00005 ( 4) ********************** 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 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 LYS 318 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 THR 335 is missing expected H atoms. Skipping. Residue TYR 359 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 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 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 528 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 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue ILE 583 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 LYS 686 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 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 LEU 749 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.671 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: A 208 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.6676 (t80) REVERT: B 208 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.6737 (t80) REVERT: C 208 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.6686 (t80) REVERT: D 208 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.6691 (t80) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.2208 time to fit residues: 71.0423 Evaluate side-chains 196 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 208 TYR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 208 TYR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 208 TYR Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 583 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146343 restraints weight = 63107.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149526 restraints weight = 40783.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151996 restraints weight = 29577.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153081 restraints weight = 23739.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154164 restraints weight = 20598.638| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 18180 Z= 0.247 Angle : 0.814 59.200 24832 Z= 0.495 Chirality : 0.034 0.263 3024 Planarity : 0.003 0.049 3088 Dihedral : 4.555 51.352 2660 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.10 % Allowed : 14.46 % Favored : 84.44 % Cbeta Deviations : 0.08 % 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: 1.07 (0.18), residues: 2412 helix: 1.68 (0.13), residues: 1644 sheet: 0.31 (0.78), residues: 64 loop : -1.65 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 416 TYR 0.013 0.002 TYR B 208 PHE 0.014 0.001 PHE A 193 TRP 0.017 0.001 TRP C 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00508 (18172) covalent geometry : angle 0.81289 (24824) SS BOND : bond 0.00064 ( 4) SS BOND : angle 2.11145 ( 8) hydrogen bonds : bond 0.04135 ( 1152) hydrogen bonds : angle 3.81198 ( 3360) Misc. bond : bond 0.00005 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.37 seconds wall clock time: 74 minutes 54.73 seconds (4494.73 seconds total)