Starting phenix.real_space_refine on Thu Mar 5 02:57:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.map" model { file = "/net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj3_33218/03_2026/7xj3_33218.cif" } resolution = 3.54 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= 0.004 sd= 0.113 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12225 2.51 5 N 3047 2.21 5 O 3109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 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: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4590 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 293 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 26, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 244 Chain: "C" Number of atoms: 4580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4580 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 254 Chain: "A" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4576 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 254 Chain: "D" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4576 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'6OU': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-2': 3, '6OU:plan-3': 3, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 4.55, per 1000 atoms: 0.25 Number of scatterers: 18493 At special positions: 0 Unit cell: (142.79, 144.97, 126.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3109 8.00 N 3047 7.00 C 12225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 892.5 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 4 sheets defined 65.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.595A pdb=" N GLY B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.355A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.904A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.717A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.508A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.523A pdb=" N MET B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.592A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.606A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.536A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 461 removed outlier: 3.509A pdb=" N HIS B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 506 removed outlier: 3.836A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 Processing helix chain 'B' and resid 546 through 560 removed outlier: 4.561A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 removed outlier: 3.531A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.503A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 667 Processing helix chain 'B' and resid 668 through 704 removed outlier: 3.674A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.609A pdb=" N ARG B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 removed outlier: 3.609A pdb=" N GLY C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 removed outlier: 4.361A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.912A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.705A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 removed outlier: 3.507A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.527A pdb=" N MET C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.592A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.599A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.527A pdb=" N ILE C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 461 removed outlier: 3.506A pdb=" N HIS C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 506 removed outlier: 3.823A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 Processing helix chain 'C' and resid 546 through 560 removed outlier: 4.403A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 568 removed outlier: 3.546A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.502A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.266A pdb=" N SER C 620 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 667 Processing helix chain 'C' and resid 668 through 704 removed outlier: 3.628A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.615A pdb=" N ARG C 716 " --> pdb=" O ARG C 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.613A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 148 removed outlier: 4.406A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.904A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.700A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.513A pdb=" N ALA A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.522A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.603A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.583A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.528A pdb=" N ILE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 461 removed outlier: 3.512A pdb=" N HIS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.851A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 Processing helix chain 'A' and resid 546 through 560 removed outlier: 4.539A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 removed outlier: 3.540A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 609 Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 668 through 704 removed outlier: 3.630A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.605A pdb=" N ARG A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.598A pdb=" N GLY D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 148 removed outlier: 4.347A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.908A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.726A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.527A pdb=" N ALA D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 316 through 327 Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.525A pdb=" N MET D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.600A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.626A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.531A pdb=" N ILE D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 461 removed outlier: 3.509A pdb=" N HIS D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 506 removed outlier: 3.832A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 Processing helix chain 'D' and resid 546 through 560 removed outlier: 4.410A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 568 removed outlier: 3.540A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 586 Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.505A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.806A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 668 through 704 removed outlier: 3.628A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU D 687 " --> pdb=" O ASN D 683 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.609A pdb=" N ARG D 716 " --> pdb=" O ARG D 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 376 through 378 removed outlier: 3.862A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.827A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.845A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 removed outlier: 3.865A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3177 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: 2.88 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.55: 18680 1.55 - 1.91: 191 1.91 - 2.27: 0 2.27 - 2.64: 0 2.64 - 3.00: 2 Bond restraints: 18873 Sorted by residual: bond pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 1.332 2.998 -1.666 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 1.332 2.997 -1.664 1.40e-02 5.10e+03 1.41e+04 bond pdb=" C PRO B 753 " pdb=" O PRO B 753 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C PRO A 753 " pdb=" O PRO A 753 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.16e-02 7.43e+03 1.75e+01 bond pdb=" C PRO D 753 " pdb=" O PRO D 753 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.16e-02 7.43e+03 1.72e+01 ... (remaining 18868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.80: 25604 10.80 - 21.60: 4 21.60 - 32.40: 4 32.40 - 43.21: 0 43.21 - 54.01: 2 Bond angle restraints: 25614 Sorted by residual: angle pdb=" O PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 122.64 68.63 54.01 1.35e+00 5.49e-01 1.60e+03 angle pdb=" O PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 122.64 68.83 53.81 1.35e+00 5.49e-01 1.59e+03 angle pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 121.54 148.46 -26.92 1.91e+00 2.74e-01 1.99e+02 angle pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 121.54 148.43 -26.89 1.91e+00 2.74e-01 1.98e+02 angle pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 116.70 142.75 -26.05 2.07e+00 2.33e-01 1.58e+02 ... (remaining 25609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 10132 24.23 - 48.45: 829 48.45 - 72.68: 73 72.68 - 96.90: 12 96.90 - 121.13: 3 Dihedral angle restraints: 11049 sinusoidal: 3919 harmonic: 7130 Sorted by residual: dihedral pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual -180.00 -65.76 -114.24 0 5.00e+00 4.00e-02 5.22e+02 dihedral pdb=" CA PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual -180.00 -66.03 -113.97 0 5.00e+00 4.00e-02 5.20e+02 dihedral pdb=" CA HIS A 585 " pdb=" C HIS A 585 " pdb=" N ASP A 586 " pdb=" CA ASP A 586 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 11046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1878 0.036 - 0.072: 901 0.072 - 0.108: 210 0.108 - 0.143: 65 0.143 - 0.179: 6 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE D 609 " pdb=" N ILE D 609 " pdb=" C ILE D 609 " pdb=" CB ILE D 609 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA ILE A 609 " pdb=" N ILE A 609 " pdb=" C ILE A 609 " pdb=" CB ILE A 609 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA GLU A 423 " pdb=" N GLU A 423 " pdb=" C GLU A 423 " pdb=" CB GLU A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 3057 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 613 " -0.169 2.00e-02 2.50e+03 1.94e-01 3.78e+02 pdb=" C PRO C 613 " 0.330 2.00e-02 2.50e+03 pdb=" O PRO C 613 " -0.101 2.00e-02 2.50e+03 pdb=" N ASN C 616 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 613 " -0.169 2.00e-02 2.50e+03 1.94e-01 3.76e+02 pdb=" C PRO B 613 " 0.329 2.00e-02 2.50e+03 pdb=" O PRO B 613 " -0.100 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 352 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C GLY A 352 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 352 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS A 353 " -0.011 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4470 2.77 - 3.31: 17020 3.31 - 3.84: 28359 3.84 - 4.37: 30839 4.37 - 4.90: 57012 Nonbonded interactions: 137700 Sorted by model distance: nonbonded pdb=" N ASN D 178 " pdb=" OD1 ASN D 178 " model vdw 2.242 3.120 nonbonded pdb=" N ASN A 178 " pdb=" OD1 ASN A 178 " model vdw 2.243 3.120 nonbonded pdb=" N ASN B 178 " pdb=" OD1 ASN B 178 " model vdw 2.248 3.120 nonbonded pdb=" CE1 TYR D 622 " pdb=" OE1 GLU D 631 " model vdw 2.251 3.340 nonbonded pdb=" OH TYR C 260 " pdb=" ND2 ASN C 297 " model vdw 2.256 3.120 ... (remaining 137695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 754 or (resid 1401 and (name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43)) or resi \ d 1403)) selection = (chain 'B' and (resid 118 through 610 or (resid 611 and (name N or name CA or na \ me C or name O or name CB )) or resid 612 through 749 or (resid 750 through 752 \ and (name N or name CA or name C or name O or name CB )) or resid 753 through 75 \ 4 or (resid 1501 and (name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C42 or name C43)) or (resid 1503 and (name C38 or name C39 or \ name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name C4 \ 6 or name C47 or name C48 or name C49)))) selection = (chain 'C' and (resid 118 through 610 or (resid 611 and (name N or name CA or na \ me C or name O or name CB )) or resid 612 through 1701 or (resid 1703 and (name \ C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or n \ ame C45 or name C46 or name C47 or name C48 or name C49)))) selection = (chain 'D' and (resid 118 through 754 or (resid 1701 and (name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43)) or (res \ id 1703 and (name C38 or name C39 or name C40 or name C41 or name C42 or name C4 \ 3 or name C44 or name C45 or name C46 or name C47 or name C48 or name C49)))) } 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: 1.070 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.030 Find NCS groups from input model: 0.450 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.019 1.666 18873 Z= 1.277 Angle : 1.030 54.007 25614 Z= 0.611 Chirality : 0.043 0.179 3060 Planarity : 0.006 0.194 3146 Dihedral : 16.434 121.126 6417 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.79 % Favored : 91.16 % Rotamer: Outliers : 6.79 % Allowed : 21.13 % Favored : 72.08 % 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: -3.52 (0.14), residues: 2388 helix: -1.44 (0.11), residues: 1536 sheet: -3.89 (0.50), residues: 56 loop : -3.90 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 690 TYR 0.023 0.002 TYR B 451 PHE 0.017 0.002 PHE C 625 TRP 0.029 0.002 TRP A 380 HIS 0.011 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.01902 (18873) covalent geometry : angle 1.03043 (25614) hydrogen bonds : bond 0.15804 ( 1080) hydrogen bonds : angle 6.02888 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 266 time to evaluate : 0.665 Fit side-chains REVERT: B 205 ASN cc_start: 0.9032 (t0) cc_final: 0.8818 (t0) REVERT: B 572 MET cc_start: 0.7875 (tpt) cc_final: 0.7545 (mmt) REVERT: B 586 ASP cc_start: 0.6808 (m-30) cc_final: 0.6059 (m-30) REVERT: B 652 ILE cc_start: 0.8473 (mp) cc_final: 0.8197 (mm) REVERT: C 299 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 358 LYS cc_start: 0.9251 (tttm) cc_final: 0.8925 (tttp) REVERT: C 396 ASP cc_start: 0.8333 (t70) cc_final: 0.8065 (t70) REVERT: C 488 MET cc_start: 0.8126 (mtm) cc_final: 0.7903 (mpp) REVERT: C 572 MET cc_start: 0.7856 (tpt) cc_final: 0.7531 (mmp) REVERT: C 586 ASP cc_start: 0.6788 (m-30) cc_final: 0.6028 (m-30) REVERT: C 652 ILE cc_start: 0.8445 (mp) cc_final: 0.8202 (mm) REVERT: A 205 ASN cc_start: 0.9033 (t0) cc_final: 0.8824 (t0) REVERT: A 320 MET cc_start: 0.8624 (mmm) cc_final: 0.8197 (mmm) REVERT: A 396 ASP cc_start: 0.8337 (t70) cc_final: 0.8073 (t70) REVERT: A 442 PHE cc_start: 0.7130 (t80) cc_final: 0.6526 (m-10) REVERT: A 562 MET cc_start: 0.8685 (mmm) cc_final: 0.8415 (mmt) REVERT: A 572 MET cc_start: 0.7874 (tpt) cc_final: 0.7568 (mmt) REVERT: A 574 MET cc_start: 0.7635 (mtt) cc_final: 0.7277 (mtt) REVERT: A 586 ASP cc_start: 0.6793 (m-30) cc_final: 0.6059 (m-30) REVERT: A 652 ILE cc_start: 0.8405 (mp) cc_final: 0.8160 (mm) REVERT: D 234 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8340 (mp) REVERT: D 320 MET cc_start: 0.8624 (mmm) cc_final: 0.8167 (mmm) REVERT: D 396 ASP cc_start: 0.8306 (t70) cc_final: 0.8037 (t70) REVERT: D 442 PHE cc_start: 0.7120 (t80) cc_final: 0.6558 (m-10) REVERT: D 572 MET cc_start: 0.7848 (tpt) cc_final: 0.7545 (mmt) REVERT: D 586 ASP cc_start: 0.6794 (m-30) cc_final: 0.6061 (m-30) outliers start: 118 outliers final: 96 residues processed: 368 average time/residue: 0.1228 time to fit residues: 72.6147 Evaluate side-chains 322 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 224 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 405 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS B 346 GLN B 410 ASN B 695 GLN C 301 HIS C 346 GLN C 410 ASN C 585 HIS A 301 HIS A 346 GLN A 410 ASN A 585 HIS D 301 HIS D 346 GLN D 410 ASN D 585 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106787 restraints weight = 24948.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109892 restraints weight = 15946.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111992 restraints weight = 12001.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113357 restraints weight = 9956.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114350 restraints weight = 8798.145| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18873 Z= 0.121 Angle : 0.504 5.631 25614 Z= 0.273 Chirality : 0.036 0.131 3060 Planarity : 0.004 0.036 3146 Dihedral : 8.314 123.847 2873 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 3.91 % Allowed : 20.03 % Favored : 76.05 % 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: -1.62 (0.16), residues: 2392 helix: 0.11 (0.13), residues: 1576 sheet: -3.20 (0.54), residues: 52 loop : -3.48 (0.16), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.011 0.001 TYR D 451 PHE 0.018 0.001 PHE C 489 TRP 0.020 0.002 TRP A 380 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00266 (18873) covalent geometry : angle 0.50388 (25614) hydrogen bonds : bond 0.04371 ( 1080) hydrogen bonds : angle 4.05754 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 0.649 Fit side-chains REVERT: B 233 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 320 MET cc_start: 0.8384 (mmm) cc_final: 0.7598 (mmm) REVERT: B 488 MET cc_start: 0.8074 (mpp) cc_final: 0.7794 (mpp) REVERT: B 562 MET cc_start: 0.8595 (tpp) cc_final: 0.8180 (mmt) REVERT: B 572 MET cc_start: 0.7297 (tpt) cc_final: 0.7061 (mmp) REVERT: B 647 ASN cc_start: 0.8052 (t0) cc_final: 0.7843 (t0) REVERT: C 233 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8638 (tt) REVERT: C 320 MET cc_start: 0.8304 (mmm) cc_final: 0.7630 (mmm) REVERT: C 358 LYS cc_start: 0.9134 (tttm) cc_final: 0.8883 (tttp) REVERT: C 488 MET cc_start: 0.7966 (mtm) cc_final: 0.7733 (mpp) REVERT: C 647 ASN cc_start: 0.8325 (t0) cc_final: 0.8077 (t0) REVERT: C 672 MET cc_start: 0.6984 (ttp) cc_final: 0.6765 (ttp) REVERT: A 233 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 320 MET cc_start: 0.8388 (mmm) cc_final: 0.7613 (mmm) REVERT: A 442 PHE cc_start: 0.6814 (t80) cc_final: 0.6081 (m-10) REVERT: A 488 MET cc_start: 0.8082 (mpp) cc_final: 0.7802 (mpp) REVERT: A 572 MET cc_start: 0.7266 (tpt) cc_final: 0.7008 (mmp) REVERT: A 647 ASN cc_start: 0.8006 (t0) cc_final: 0.7698 (t0) REVERT: D 320 MET cc_start: 0.8382 (mmm) cc_final: 0.7598 (mmm) REVERT: D 442 PHE cc_start: 0.6775 (t80) cc_final: 0.6117 (m-10) REVERT: D 488 MET cc_start: 0.8064 (mpp) cc_final: 0.7710 (mpp) REVERT: D 652 ILE cc_start: 0.8249 (mp) cc_final: 0.7873 (mm) REVERT: D 672 MET cc_start: 0.6954 (ttp) cc_final: 0.6603 (ttp) outliers start: 68 outliers final: 35 residues processed: 312 average time/residue: 0.1288 time to fit residues: 63.3527 Evaluate side-chains 269 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 681 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 ASN C 178 ASN C 410 ASN A 410 ASN D 410 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103010 restraints weight = 25282.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106045 restraints weight = 16333.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108067 restraints weight = 12349.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.109299 restraints weight = 10305.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110323 restraints weight = 9168.901| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18873 Z= 0.112 Angle : 0.491 8.170 25614 Z= 0.258 Chirality : 0.036 0.149 3060 Planarity : 0.003 0.040 3146 Dihedral : 6.507 109.125 2740 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 3.45 % Allowed : 23.14 % Favored : 73.40 % 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: -0.80 (0.17), residues: 2392 helix: 0.76 (0.14), residues: 1576 sheet: -2.67 (0.53), residues: 52 loop : -3.21 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 693 TYR 0.014 0.001 TYR A 575 PHE 0.010 0.001 PHE C 489 TRP 0.016 0.001 TRP A 380 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00249 (18873) covalent geometry : angle 0.49128 (25614) hydrogen bonds : bond 0.04008 ( 1080) hydrogen bonds : angle 3.77835 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.682 Fit side-chains REVERT: B 320 MET cc_start: 0.8398 (mmm) cc_final: 0.7677 (mmm) REVERT: B 488 MET cc_start: 0.8034 (mpp) cc_final: 0.7765 (mpp) REVERT: C 157 PHE cc_start: 0.8393 (t80) cc_final: 0.8141 (t80) REVERT: C 234 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 320 MET cc_start: 0.8332 (mmm) cc_final: 0.7738 (mmm) REVERT: C 488 MET cc_start: 0.8002 (mtm) cc_final: 0.7728 (mpp) REVERT: A 159 MET cc_start: 0.8293 (mmp) cc_final: 0.7739 (mmp) REVERT: A 320 MET cc_start: 0.8399 (mmm) cc_final: 0.7710 (mmm) REVERT: A 488 MET cc_start: 0.8123 (mpp) cc_final: 0.7842 (mpp) REVERT: A 555 MET cc_start: 0.7114 (ttp) cc_final: 0.6730 (mtp) REVERT: D 157 PHE cc_start: 0.8375 (t80) cc_final: 0.8142 (t80) REVERT: D 320 MET cc_start: 0.8393 (mmm) cc_final: 0.7669 (mmm) REVERT: D 488 MET cc_start: 0.8014 (mpp) cc_final: 0.7673 (mpp) REVERT: D 555 MET cc_start: 0.7143 (ttp) cc_final: 0.6839 (ttm) REVERT: D 647 ASN cc_start: 0.7931 (t0) cc_final: 0.7644 (t0) REVERT: D 652 ILE cc_start: 0.8234 (mp) cc_final: 0.7908 (mm) REVERT: D 672 MET cc_start: 0.7009 (ttp) cc_final: 0.6684 (ttp) outliers start: 60 outliers final: 39 residues processed: 293 average time/residue: 0.1223 time to fit residues: 58.0715 Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 284 HIS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 96 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 452 ASN D 339 ASN D 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105765 restraints weight = 25204.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108783 restraints weight = 16153.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110866 restraints weight = 12197.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112177 restraints weight = 10113.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113167 restraints weight = 8955.663| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18873 Z= 0.145 Angle : 0.519 6.299 25614 Z= 0.272 Chirality : 0.037 0.124 3060 Planarity : 0.003 0.041 3146 Dihedral : 6.338 104.345 2736 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 4.38 % Allowed : 23.20 % Favored : 72.42 % 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: -0.45 (0.17), residues: 2392 helix: 1.01 (0.14), residues: 1576 sheet: -2.32 (0.57), residues: 52 loop : -3.06 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 693 TYR 0.016 0.001 TYR D 451 PHE 0.010 0.001 PHE B 316 TRP 0.014 0.001 TRP A 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00346 (18873) covalent geometry : angle 0.51949 (25614) hydrogen bonds : bond 0.04216 ( 1080) hydrogen bonds : angle 3.72623 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.618 Fit side-chains REVERT: B 320 MET cc_start: 0.8382 (mmm) cc_final: 0.7642 (mmm) REVERT: B 488 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7750 (mpp) REVERT: B 701 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8120 (mt) REVERT: C 157 PHE cc_start: 0.8315 (t80) cc_final: 0.8079 (t80) REVERT: C 234 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8240 (mp) REVERT: C 320 MET cc_start: 0.8331 (mmm) cc_final: 0.7658 (mmm) REVERT: C 488 MET cc_start: 0.7981 (mtm) cc_final: 0.7668 (mpp) REVERT: C 572 MET cc_start: 0.7089 (mmm) cc_final: 0.6867 (mmp) REVERT: A 159 MET cc_start: 0.8122 (mmp) cc_final: 0.7591 (mmp) REVERT: A 320 MET cc_start: 0.8376 (mmm) cc_final: 0.7672 (mmm) REVERT: A 488 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7781 (mpp) REVERT: D 320 MET cc_start: 0.8371 (mmm) cc_final: 0.7628 (mmm) REVERT: D 358 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8562 (tttp) REVERT: D 488 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7714 (mpp) REVERT: D 572 MET cc_start: 0.7221 (mmm) cc_final: 0.6864 (mmp) REVERT: D 647 ASN cc_start: 0.7920 (t0) cc_final: 0.7611 (t0) REVERT: D 652 ILE cc_start: 0.8316 (mp) cc_final: 0.8022 (mm) REVERT: D 672 MET cc_start: 0.6951 (ttp) cc_final: 0.6731 (ttp) REVERT: D 701 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8109 (mt) outliers start: 76 outliers final: 58 residues processed: 268 average time/residue: 0.1191 time to fit residues: 51.4931 Evaluate side-chains 270 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 12 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN B 452 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103627 restraints weight = 25070.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106652 restraints weight = 16152.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108677 restraints weight = 12203.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109932 restraints weight = 10177.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110874 restraints weight = 9050.973| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18873 Z= 0.105 Angle : 0.466 5.858 25614 Z= 0.246 Chirality : 0.036 0.165 3060 Planarity : 0.003 0.040 3146 Dihedral : 5.919 91.624 2734 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 4.15 % Allowed : 23.32 % Favored : 72.54 % 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: -0.14 (0.17), residues: 2392 helix: 1.22 (0.14), residues: 1580 sheet: -2.09 (0.55), residues: 52 loop : -2.89 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 693 TYR 0.013 0.001 TYR D 575 PHE 0.020 0.001 PHE D 157 TRP 0.013 0.001 TRP B 380 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00232 (18873) covalent geometry : angle 0.46604 (25614) hydrogen bonds : bond 0.03686 ( 1080) hydrogen bonds : angle 3.59977 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.708 Fit side-chains REVERT: B 320 MET cc_start: 0.8412 (mmm) cc_final: 0.7726 (mmm) REVERT: B 488 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7728 (mpp) REVERT: B 572 MET cc_start: 0.7333 (mmm) cc_final: 0.6968 (mmp) REVERT: B 672 MET cc_start: 0.6789 (ttp) cc_final: 0.6291 (ttp) REVERT: B 701 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8129 (mt) REVERT: C 320 MET cc_start: 0.8339 (mmm) cc_final: 0.7757 (mmm) REVERT: C 488 MET cc_start: 0.7890 (mtm) cc_final: 0.7630 (mpp) REVERT: A 159 MET cc_start: 0.8264 (mmp) cc_final: 0.7729 (mmp) REVERT: A 320 MET cc_start: 0.8398 (mmm) cc_final: 0.7777 (mmm) REVERT: A 488 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7785 (mpp) REVERT: D 320 MET cc_start: 0.8392 (mmm) cc_final: 0.7735 (mmm) REVERT: D 488 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7659 (mpp) REVERT: D 652 ILE cc_start: 0.8264 (mp) cc_final: 0.7980 (mm) REVERT: D 701 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8145 (mt) outliers start: 72 outliers final: 52 residues processed: 291 average time/residue: 0.1204 time to fit residues: 55.8007 Evaluate side-chains 270 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 163 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN B 647 ASN C 339 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN D 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109628 restraints weight = 24833.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112753 restraints weight = 15970.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114892 restraints weight = 12003.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116129 restraints weight = 9942.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117178 restraints weight = 8831.982| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18873 Z= 0.094 Angle : 0.454 7.376 25614 Z= 0.238 Chirality : 0.035 0.136 3060 Planarity : 0.003 0.039 3146 Dihedral : 5.424 71.346 2728 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 4.09 % Allowed : 24.18 % Favored : 71.73 % 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: 0.14 (0.17), residues: 2392 helix: 1.42 (0.14), residues: 1576 sheet: -1.93 (0.52), residues: 52 loop : -2.74 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 698 TYR 0.012 0.001 TYR D 575 PHE 0.020 0.001 PHE A 157 TRP 0.013 0.001 TRP B 380 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00198 (18873) covalent geometry : angle 0.45373 (25614) hydrogen bonds : bond 0.03376 ( 1080) hydrogen bonds : angle 3.50469 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 0.709 Fit side-chains REVERT: B 320 MET cc_start: 0.8366 (mmm) cc_final: 0.7668 (mmm) REVERT: B 488 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: B 572 MET cc_start: 0.7197 (mmm) cc_final: 0.6841 (mmt) REVERT: B 701 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 320 MET cc_start: 0.8305 (mmm) cc_final: 0.7700 (mmm) REVERT: C 488 MET cc_start: 0.7850 (mtm) cc_final: 0.7589 (mpp) REVERT: C 672 MET cc_start: 0.6694 (ttp) cc_final: 0.6209 (ttp) REVERT: A 159 MET cc_start: 0.8080 (mmp) cc_final: 0.7599 (mmp) REVERT: A 320 MET cc_start: 0.8353 (mmm) cc_final: 0.7691 (mmm) REVERT: A 488 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: A 572 MET cc_start: 0.7065 (mmm) cc_final: 0.6752 (mmt) REVERT: A 621 SER cc_start: 0.8921 (m) cc_final: 0.8507 (p) REVERT: D 320 MET cc_start: 0.8349 (mmm) cc_final: 0.7645 (mmm) REVERT: D 358 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8555 (tttp) REVERT: D 488 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7601 (mpp) REVERT: D 572 MET cc_start: 0.7101 (mmm) cc_final: 0.6805 (mmp) REVERT: D 652 ILE cc_start: 0.8250 (mp) cc_final: 0.7976 (mm) REVERT: D 701 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7993 (mt) outliers start: 71 outliers final: 51 residues processed: 297 average time/residue: 0.1229 time to fit residues: 58.9871 Evaluate side-chains 289 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 149 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102561 restraints weight = 25401.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105420 restraints weight = 16702.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107373 restraints weight = 12806.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108543 restraints weight = 10748.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109525 restraints weight = 9601.092| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18873 Z= 0.136 Angle : 0.505 8.483 25614 Z= 0.261 Chirality : 0.036 0.122 3060 Planarity : 0.003 0.040 3146 Dihedral : 5.609 71.616 2728 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.32 % Allowed : 24.87 % Favored : 70.81 % 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: 0.11 (0.17), residues: 2392 helix: 1.38 (0.14), residues: 1580 sheet: -1.81 (0.51), residues: 52 loop : -2.74 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 698 TYR 0.015 0.001 TYR A 451 PHE 0.020 0.001 PHE B 489 TRP 0.012 0.001 TRP B 380 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00320 (18873) covalent geometry : angle 0.50541 (25614) hydrogen bonds : bond 0.03889 ( 1080) hydrogen bonds : angle 3.57045 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 235 time to evaluate : 0.692 Fit side-chains REVERT: B 320 MET cc_start: 0.8386 (mmm) cc_final: 0.7712 (mmm) REVERT: B 488 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: C 320 MET cc_start: 0.8356 (mmm) cc_final: 0.7729 (mmm) REVERT: C 488 MET cc_start: 0.7897 (mtm) cc_final: 0.7609 (mpp) REVERT: C 555 MET cc_start: 0.7177 (tpp) cc_final: 0.6747 (tpp) REVERT: C 672 MET cc_start: 0.6643 (ttp) cc_final: 0.6186 (ttp) REVERT: A 320 MET cc_start: 0.8396 (mmm) cc_final: 0.7756 (mmm) REVERT: A 358 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8539 (tttp) REVERT: A 488 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: A 555 MET cc_start: 0.7175 (tpp) cc_final: 0.6769 (tpp) REVERT: A 621 SER cc_start: 0.8951 (m) cc_final: 0.8497 (p) REVERT: D 320 MET cc_start: 0.8377 (mmm) cc_final: 0.7702 (mmm) REVERT: D 358 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8533 (tttp) REVERT: D 488 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7717 (mpp) REVERT: D 572 MET cc_start: 0.7057 (mmm) cc_final: 0.6826 (mmp) REVERT: D 652 ILE cc_start: 0.8261 (mp) cc_final: 0.7982 (mm) REVERT: D 672 MET cc_start: 0.6715 (ttp) cc_final: 0.6501 (ttp) REVERT: D 701 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8116 (mt) outliers start: 75 outliers final: 61 residues processed: 285 average time/residue: 0.1260 time to fit residues: 57.6610 Evaluate side-chains 281 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104685 restraints weight = 25022.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107676 restraints weight = 16202.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109499 restraints weight = 12294.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111003 restraints weight = 10319.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111737 restraints weight = 9131.816| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18873 Z= 0.109 Angle : 0.482 9.062 25614 Z= 0.249 Chirality : 0.035 0.121 3060 Planarity : 0.003 0.037 3146 Dihedral : 5.455 73.267 2728 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.26 % Allowed : 24.93 % Favored : 70.81 % 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: 0.20 (0.17), residues: 2392 helix: 1.46 (0.14), residues: 1580 sheet: -1.63 (0.50), residues: 52 loop : -2.71 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 698 TYR 0.014 0.001 TYR A 451 PHE 0.020 0.001 PHE D 157 TRP 0.012 0.001 TRP B 380 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00246 (18873) covalent geometry : angle 0.48151 (25614) hydrogen bonds : bond 0.03638 ( 1080) hydrogen bonds : angle 3.51163 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 0.710 Fit side-chains REVERT: B 320 MET cc_start: 0.8404 (mmm) cc_final: 0.7755 (mmm) REVERT: B 488 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7693 (mpp) REVERT: C 320 MET cc_start: 0.8352 (mmm) cc_final: 0.7749 (mmm) REVERT: C 488 MET cc_start: 0.7854 (mtm) cc_final: 0.7588 (mpp) REVERT: C 555 MET cc_start: 0.7219 (tpp) cc_final: 0.6847 (tpp) REVERT: C 672 MET cc_start: 0.6798 (ttp) cc_final: 0.6325 (ttp) REVERT: A 320 MET cc_start: 0.8393 (mmm) cc_final: 0.7776 (mmm) REVERT: A 358 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: A 488 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7739 (mpp) REVERT: A 621 SER cc_start: 0.8973 (m) cc_final: 0.8550 (p) REVERT: D 213 TYR cc_start: 0.8710 (m-80) cc_final: 0.8261 (m-10) REVERT: D 320 MET cc_start: 0.8384 (mmm) cc_final: 0.7726 (mmm) REVERT: D 358 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8568 (tttp) REVERT: D 488 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7625 (mpp) REVERT: D 572 MET cc_start: 0.7147 (mmm) cc_final: 0.6883 (mmp) REVERT: D 652 ILE cc_start: 0.8267 (mp) cc_final: 0.7994 (mm) REVERT: D 701 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8180 (mt) outliers start: 74 outliers final: 62 residues processed: 276 average time/residue: 0.1233 time to fit residues: 54.8972 Evaluate side-chains 289 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 521 TRP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 178 ASN Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 521 TRP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 137 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109132 restraints weight = 24849.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112375 restraints weight = 15643.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114566 restraints weight = 11661.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115931 restraints weight = 9599.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116802 restraints weight = 8481.590| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18873 Z= 0.096 Angle : 0.472 9.366 25614 Z= 0.242 Chirality : 0.035 0.125 3060 Planarity : 0.003 0.036 3146 Dihedral : 5.255 76.217 2728 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.74 % Allowed : 25.56 % Favored : 70.70 % 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: 0.38 (0.17), residues: 2392 helix: 1.59 (0.14), residues: 1580 sheet: -1.56 (0.49), residues: 52 loop : -2.64 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 698 TYR 0.015 0.001 TYR C 575 PHE 0.020 0.001 PHE D 157 TRP 0.012 0.001 TRP B 380 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00206 (18873) covalent geometry : angle 0.47190 (25614) hydrogen bonds : bond 0.03396 ( 1080) hydrogen bonds : angle 3.45661 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.709 Fit side-chains REVERT: B 320 MET cc_start: 0.8373 (mmm) cc_final: 0.7695 (mmm) REVERT: B 401 ASN cc_start: 0.8292 (p0) cc_final: 0.8010 (p0) REVERT: B 488 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: C 320 MET cc_start: 0.8307 (mmm) cc_final: 0.7717 (mmm) REVERT: C 401 ASN cc_start: 0.8247 (p0) cc_final: 0.7971 (p0) REVERT: C 488 MET cc_start: 0.7858 (mtm) cc_final: 0.7578 (mpp) REVERT: C 672 MET cc_start: 0.6480 (ttp) cc_final: 0.6068 (ttp) REVERT: A 320 MET cc_start: 0.8369 (mmm) cc_final: 0.7726 (mmm) REVERT: A 358 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8502 (tttp) REVERT: A 401 ASN cc_start: 0.8219 (p0) cc_final: 0.7962 (p0) REVERT: A 488 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: A 621 SER cc_start: 0.8921 (m) cc_final: 0.8518 (p) REVERT: D 213 TYR cc_start: 0.8692 (m-80) cc_final: 0.8228 (m-10) REVERT: D 320 MET cc_start: 0.8354 (mmm) cc_final: 0.7677 (mmm) REVERT: D 358 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8566 (tttp) REVERT: D 401 ASN cc_start: 0.8256 (p0) cc_final: 0.8018 (p0) REVERT: D 488 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7598 (mpp) REVERT: D 572 MET cc_start: 0.7030 (mmm) cc_final: 0.6770 (mmp) REVERT: D 652 ILE cc_start: 0.8238 (mp) cc_final: 0.7965 (mm) REVERT: D 701 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7969 (mt) outliers start: 65 outliers final: 47 residues processed: 275 average time/residue: 0.1251 time to fit residues: 55.2534 Evaluate side-chains 275 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 225 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 647 ASN ** 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 = 0.3522 r_free = 0.3522 target = 0.138536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106512 restraints weight = 24938.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109362 restraints weight = 16135.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111555 restraints weight = 12260.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112764 restraints weight = 10183.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113803 restraints weight = 9063.882| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18873 Z= 0.106 Angle : 0.485 9.410 25614 Z= 0.247 Chirality : 0.035 0.122 3060 Planarity : 0.003 0.036 3146 Dihedral : 5.012 78.215 2720 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.34 % Allowed : 26.08 % Favored : 70.58 % 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: 0.46 (0.17), residues: 2392 helix: 1.64 (0.14), residues: 1580 sheet: -1.44 (0.50), residues: 52 loop : -2.59 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 698 TYR 0.014 0.001 TYR C 575 PHE 0.020 0.001 PHE D 157 TRP 0.012 0.001 TRP B 380 HIS 0.004 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00237 (18873) covalent geometry : angle 0.48540 (25614) hydrogen bonds : bond 0.03487 ( 1080) hydrogen bonds : angle 3.45481 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.722 Fit side-chains REVERT: B 213 TYR cc_start: 0.8667 (m-80) cc_final: 0.8194 (m-10) REVERT: B 320 MET cc_start: 0.8364 (mmm) cc_final: 0.7711 (mmm) REVERT: B 401 ASN cc_start: 0.8280 (p0) cc_final: 0.7997 (p0) REVERT: B 488 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7712 (mpp) REVERT: C 320 MET cc_start: 0.8338 (mmm) cc_final: 0.7736 (mmm) REVERT: C 401 ASN cc_start: 0.8249 (p0) cc_final: 0.7971 (p0) REVERT: C 488 MET cc_start: 0.7856 (mtm) cc_final: 0.7572 (mpp) REVERT: C 672 MET cc_start: 0.6455 (ttp) cc_final: 0.6037 (ttp) REVERT: A 320 MET cc_start: 0.8394 (mmm) cc_final: 0.7743 (mmm) REVERT: A 358 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8487 (tttp) REVERT: A 401 ASN cc_start: 0.8203 (p0) cc_final: 0.7933 (p0) REVERT: A 488 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7735 (mpp) REVERT: A 621 SER cc_start: 0.8919 (m) cc_final: 0.8489 (p) REVERT: D 213 TYR cc_start: 0.8701 (m-80) cc_final: 0.8209 (m-10) REVERT: D 320 MET cc_start: 0.8377 (mmm) cc_final: 0.7696 (mmm) REVERT: D 358 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8536 (tttp) REVERT: D 401 ASN cc_start: 0.8253 (p0) cc_final: 0.8004 (p0) REVERT: D 488 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7605 (mpp) REVERT: D 572 MET cc_start: 0.7010 (mmm) cc_final: 0.6761 (mmp) REVERT: D 652 ILE cc_start: 0.8232 (mp) cc_final: 0.7963 (mm) REVERT: D 701 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8088 (mt) outliers start: 58 outliers final: 47 residues processed: 259 average time/residue: 0.1215 time to fit residues: 50.9862 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 284 HIS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 202 optimal weight: 0.0030 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109181 restraints weight = 24885.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112312 restraints weight = 15895.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114432 restraints weight = 11947.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115880 restraints weight = 9894.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116706 restraints weight = 8721.604| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18873 Z= 0.096 Angle : 0.473 9.243 25614 Z= 0.240 Chirality : 0.035 0.119 3060 Planarity : 0.003 0.035 3146 Dihedral : 4.900 83.499 2720 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.11 % Allowed : 26.42 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2392 helix: 1.72 (0.14), residues: 1580 sheet: -1.40 (0.50), residues: 52 loop : -2.53 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 698 TYR 0.015 0.001 TYR A 451 PHE 0.020 0.001 PHE D 157 TRP 0.011 0.001 TRP B 380 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00207 (18873) covalent geometry : angle 0.47270 (25614) hydrogen bonds : bond 0.03305 ( 1080) hydrogen bonds : angle 3.40924 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3016.08 seconds wall clock time: 52 minutes 48.70 seconds (3168.70 seconds total)