Starting phenix.real_space_refine on Tue Feb 13 17:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fc7_28975/02_2024/8fc7_28975_neut_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5096 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 136 5.16 5 C 16604 2.51 5 N 4304 2.21 5 O 4580 1.98 5 H 24944 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 183": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50580 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10006 Classifications: {'peptide': 631} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 606} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "F" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "H" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2576 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 10006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10006 Classifications: {'peptide': 631} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 606} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 10006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10006 Classifications: {'peptide': 631} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 606} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 10006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 10006 Classifications: {'peptide': 631} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 606} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'XPW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.15, per 1000 atoms: 0.32 Number of scatterers: 50580 At special positions: 0 Unit cell: (214.92, 214.92, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 136 16.00 P 8 15.00 Mg 4 11.99 O 4580 8.00 N 4304 7.00 C 16604 6.00 H 24944 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 29.28 Conformation dependent library (CDL) restraints added in 3.8 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 8 sheets defined 56.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.29 Creating SS restraints... Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.906A pdb=" N ASP A 167 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 170 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.280A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 336 through 356 removed outlier: 4.438A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.654A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.814A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 402' Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.752A pdb=" N HIS A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 490 removed outlier: 4.431A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 534 Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.876A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 595 removed outlier: 4.752A pdb=" N LEU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 611 removed outlier: 3.671A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 635 removed outlier: 3.693A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'A' and resid 683 through 689 removed outlier: 4.735A pdb=" N THR A 689 " --> pdb=" O MET A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 747 removed outlier: 3.940A pdb=" N THR A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 722 " --> pdb=" O MET A 718 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 66 through 73 Proline residue: E 71 - end of helix Processing helix chain 'E' and resid 89 through 97 removed outlier: 3.931A pdb=" N GLU E 93 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN E 94 " --> pdb=" O SER E 91 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 99 through 106 Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.501A pdb=" N ASN E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.882A pdb=" N MET E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 150 Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 66 through 73 Proline residue: F 71 - end of helix Processing helix chain 'F' and resid 89 through 97 removed outlier: 3.931A pdb=" N GLU F 93 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN F 94 " --> pdb=" O SER F 91 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.501A pdb=" N ASN F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.884A pdb=" N MET F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 150 Processing helix chain 'F' and resid 167 through 179 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 66 through 73 Proline residue: G 71 - end of helix Processing helix chain 'G' and resid 89 through 97 removed outlier: 3.932A pdb=" N GLU G 93 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN G 94 " --> pdb=" O SER G 91 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.501A pdb=" N ASN G 123 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.882A pdb=" N MET G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 150 Processing helix chain 'G' and resid 167 through 179 Processing helix chain 'H' and resid 18 through 27 Processing helix chain 'H' and resid 66 through 73 Proline residue: H 71 - end of helix Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.931A pdb=" N GLU H 93 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN H 94 " --> pdb=" O SER H 91 " (cutoff:3.500A) Proline residue: H 96 - end of helix Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 125 through 134 removed outlier: 3.883A pdb=" N MET H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 150 Processing helix chain 'H' and resid 167 through 179 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.906A pdb=" N ASP B 167 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY B 168 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 170 " --> pdb=" O ASP B 167 " (cutoff:3.500A) Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.280A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 336 through 356 removed outlier: 4.437A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.654A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.814A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 402' Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.752A pdb=" N HIS B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 490 removed outlier: 4.430A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 534 Processing helix chain 'B' and resid 547 through 569 removed outlier: 3.875A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 removed outlier: 4.753A pdb=" N LEU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.671A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 635 removed outlier: 3.693A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'B' and resid 683 through 689 removed outlier: 4.735A pdb=" N THR B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 747 removed outlier: 3.941A pdb=" N THR B 721 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 722 " --> pdb=" O MET B 718 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 724 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS B 727 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 163 through 175 removed outlier: 3.906A pdb=" N ASP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY C 168 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 170 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.281A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 336 through 356 removed outlier: 4.438A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.654A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.815A pdb=" N ARG C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 443 through 451 removed outlier: 4.753A pdb=" N HIS C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 490 removed outlier: 4.431A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 534 Processing helix chain 'C' and resid 547 through 569 removed outlier: 3.875A pdb=" N ALA C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 595 removed outlier: 4.752A pdb=" N LEU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 611 removed outlier: 3.671A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 635 removed outlier: 3.693A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 678 Processing helix chain 'C' and resid 683 through 689 removed outlier: 4.735A pdb=" N THR C 689 " --> pdb=" O MET C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 747 removed outlier: 3.940A pdb=" N THR C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 722 " --> pdb=" O MET C 718 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 724 " --> pdb=" O GLU C 720 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 755 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 175 removed outlier: 3.906A pdb=" N ASP D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY D 168 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 170 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Proline residue: D 171 - end of helix Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.280A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 336 through 356 removed outlier: 4.437A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 373 through 378 Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.654A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.815A pdb=" N ARG D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS D 401 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 397 through 402' Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 443 through 451 removed outlier: 4.753A pdb=" N HIS D 447 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLU D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA D 451 " --> pdb=" O HIS D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 490 removed outlier: 4.431A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 470 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 534 Processing helix chain 'D' and resid 547 through 569 removed outlier: 3.876A pdb=" N ALA D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 removed outlier: 4.752A pdb=" N LEU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 611 removed outlier: 3.671A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.693A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 678 Processing helix chain 'D' and resid 683 through 689 removed outlier: 4.736A pdb=" N THR D 689 " --> pdb=" O MET D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 747 removed outlier: 3.941A pdb=" N THR D 721 " --> pdb=" O LEU D 717 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL D 722 " --> pdb=" O MET D 718 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 724 " --> pdb=" O GLU D 720 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 727 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 755 Processing sheet with id= A, first strand: chain 'A' and resid 777 through 782 removed outlier: 6.397A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 155 through 159 removed outlier: 4.084A pdb=" N GLY E 155 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET E 157 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 155 through 159 removed outlier: 4.084A pdb=" N GLY F 155 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET F 157 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR F 42 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 155 through 159 removed outlier: 4.084A pdb=" N GLY G 155 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET G 157 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR G 42 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 155 through 159 removed outlier: 4.083A pdb=" N GLY H 155 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET H 157 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 42 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 777 through 782 removed outlier: 6.398A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 777 through 782 removed outlier: 6.397A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 777 through 782 removed outlier: 6.397A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) 1209 hydrogen bonds defined for protein. 3504 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: 16.77 Time building geometry restraints manager: 30.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5780 1.02 - 1.22: 19136 1.22 - 1.42: 10984 1.42 - 1.62: 15064 1.62 - 1.82: 216 Bond restraints: 51180 Sorted by residual: bond pdb=" C13 XPW D1001 " pdb=" O32 XPW D1001 " ideal model delta sigma weight residual 0.602 1.432 -0.830 2.00e-02 2.50e+03 1.72e+03 bond pdb=" C13 XPW A1001 " pdb=" O32 XPW A1001 " ideal model delta sigma weight residual 0.602 1.432 -0.830 2.00e-02 2.50e+03 1.72e+03 bond pdb=" C13 XPW C1001 " pdb=" O32 XPW C1001 " ideal model delta sigma weight residual 0.602 1.431 -0.829 2.00e-02 2.50e+03 1.72e+03 bond pdb=" C13 XPW B1001 " pdb=" O32 XPW B1001 " ideal model delta sigma weight residual 0.602 1.431 -0.829 2.00e-02 2.50e+03 1.72e+03 bond pdb=" C33 XPW B1001 " pdb=" N11 XPW B1001 " ideal model delta sigma weight residual 0.867 1.462 -0.595 2.00e-02 2.50e+03 8.86e+02 ... (remaining 51175 not shown) Histogram of bond angle deviations from ideal: 99.30 - 115.43: 64442 115.43 - 131.56: 27850 131.56 - 147.70: 56 147.70 - 163.83: 0 163.83 - 179.97: 4 Bond angle restraints: 92352 Sorted by residual: angle pdb=" C SER F 188 " pdb=" N GLY F 189 " pdb=" CA GLY F 189 " ideal model delta sigma weight residual 120.10 126.95 -6.85 9.50e-01 1.11e+00 5.20e+01 angle pdb=" C SER G 188 " pdb=" N GLY G 189 " pdb=" CA GLY G 189 " ideal model delta sigma weight residual 120.10 126.92 -6.82 9.50e-01 1.11e+00 5.15e+01 angle pdb=" C SER E 188 " pdb=" N GLY E 189 " pdb=" CA GLY E 189 " ideal model delta sigma weight residual 120.10 126.91 -6.81 9.50e-01 1.11e+00 5.14e+01 angle pdb=" C SER H 188 " pdb=" N GLY H 189 " pdb=" CA GLY H 189 " ideal model delta sigma weight residual 120.10 126.87 -6.77 9.50e-01 1.11e+00 5.08e+01 angle pdb=" C19 XPW A1001 " pdb=" N20 XPW A1001 " pdb=" C21 XPW A1001 " ideal model delta sigma weight residual 112.36 125.98 -13.62 3.00e+00 1.11e-01 2.06e+01 ... (remaining 92347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 23294 30.14 - 60.27: 950 60.27 - 90.41: 76 90.41 - 120.55: 0 120.55 - 150.68: 8 Dihedral angle restraints: 24328 sinusoidal: 12876 harmonic: 11452 Sorted by residual: dihedral pdb=" C18 XPW D1001 " pdb=" C17 XPW D1001 " pdb=" C19 XPW D1001 " pdb=" N20 XPW D1001 " ideal model delta sinusoidal sigma weight residual -81.77 68.91 -150.68 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C18 XPW C1001 " pdb=" C17 XPW C1001 " pdb=" C19 XPW C1001 " pdb=" N20 XPW C1001 " ideal model delta sinusoidal sigma weight residual -81.77 68.90 -150.67 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C18 XPW B1001 " pdb=" C17 XPW B1001 " pdb=" C19 XPW B1001 " pdb=" N20 XPW B1001 " ideal model delta sinusoidal sigma weight residual -81.77 68.90 -150.67 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 24325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 4100 0.358 - 0.716: 0 0.716 - 1.073: 0 1.073 - 1.431: 0 1.431 - 1.789: 4 Chirality restraints: 4104 Sorted by residual: chirality pdb=" C13 XPW A1001 " pdb=" C12 XPW A1001 " pdb=" C14 XPW A1001 " pdb=" O32 XPW A1001 " both_signs ideal model delta sigma weight residual False -0.77 -2.55 1.79 2.00e-01 2.50e+01 8.00e+01 chirality pdb=" C13 XPW D1001 " pdb=" C12 XPW D1001 " pdb=" C14 XPW D1001 " pdb=" O32 XPW D1001 " both_signs ideal model delta sigma weight residual False -0.77 -2.55 1.79 2.00e-01 2.50e+01 8.00e+01 chirality pdb=" C13 XPW B1001 " pdb=" C12 XPW B1001 " pdb=" C14 XPW B1001 " pdb=" O32 XPW B1001 " both_signs ideal model delta sigma weight residual False -0.77 -2.55 1.79 2.00e-01 2.50e+01 8.00e+01 ... (remaining 4101 not shown) Planarity restraints: 7612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 94 " -0.323 2.00e-02 2.50e+03 4.27e-01 2.73e+03 pdb=" CG ASN G 94 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN G 94 " 0.314 2.00e-02 2.50e+03 pdb=" ND2 ASN G 94 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN G 94 " 0.658 2.00e-02 2.50e+03 pdb="HD22 ASN G 94 " -0.675 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 94 " -0.323 2.00e-02 2.50e+03 4.27e-01 2.73e+03 pdb=" CG ASN E 94 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 94 " 0.314 2.00e-02 2.50e+03 pdb=" ND2 ASN E 94 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN E 94 " 0.658 2.00e-02 2.50e+03 pdb="HD22 ASN E 94 " -0.675 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 94 " -0.324 2.00e-02 2.50e+03 4.27e-01 2.73e+03 pdb=" CG ASN H 94 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN H 94 " 0.314 2.00e-02 2.50e+03 pdb=" ND2 ASN H 94 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN H 94 " 0.658 2.00e-02 2.50e+03 pdb="HD22 ASN H 94 " -0.675 2.00e-02 2.50e+03 ... (remaining 7609 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 1908 2.06 - 2.69: 71009 2.69 - 3.33: 146407 3.33 - 3.96: 186010 3.96 - 4.60: 280479 Nonbonded interactions: 685813 Sorted by model distance: nonbonded pdb=" O GLY C 600 " pdb=" HG SER C 603 " model vdw 1.424 1.850 nonbonded pdb=" O GLY A 600 " pdb=" HG SER A 603 " model vdw 1.424 1.850 nonbonded pdb=" O GLY B 600 " pdb=" HG SER B 603 " model vdw 1.424 1.850 nonbonded pdb=" O GLY D 600 " pdb=" HG SER D 603 " model vdw 1.424 1.850 nonbonded pdb=" OE1 GLU G 93 " pdb=" H GLU G 93 " model vdw 1.489 1.850 ... (remaining 685808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.560 Extract box with map and model: 5.340 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 117.470 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.250 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.015 0.830 26236 Z= 1.010 Angle : 0.781 13.621 35720 Z= 0.442 Chirality : 0.072 1.789 4104 Planarity : 0.007 0.085 4480 Dihedral : 14.886 150.685 9444 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3260 helix: 1.13 (0.12), residues: 1736 sheet: -0.94 (0.31), residues: 268 loop : -1.07 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 409 HIS 0.004 0.001 HIS D 326 PHE 0.016 0.002 PHE C 231 TYR 0.020 0.002 TYR D 236 ARG 0.008 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 554 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7681 (m110) cc_final: 0.7393 (m110) REVERT: A 219 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7770 (ttm-80) REVERT: A 224 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7024 (tpp-160) REVERT: A 531 ASP cc_start: 0.5380 (t70) cc_final: 0.5098 (t70) REVERT: A 625 MET cc_start: 0.6979 (ttt) cc_final: 0.6425 (tmm) REVERT: A 626 ILE cc_start: 0.7584 (tt) cc_final: 0.7230 (tt) REVERT: A 747 SER cc_start: 0.8488 (m) cc_final: 0.8102 (p) REVERT: E 40 GLU cc_start: 0.6189 (pt0) cc_final: 0.5814 (pt0) REVERT: E 70 ARG cc_start: 0.6572 (ttm170) cc_final: 0.6341 (ttp-170) REVERT: E 74 TYR cc_start: 0.7663 (m-10) cc_final: 0.7390 (m-10) REVERT: E 98 LYS cc_start: 0.7202 (tmtt) cc_final: 0.6873 (tptp) REVERT: E 102 GLU cc_start: 0.6396 (tt0) cc_final: 0.5962 (tt0) REVERT: E 165 ASP cc_start: 0.6122 (m-30) cc_final: 0.5895 (m-30) REVERT: F 40 GLU cc_start: 0.6193 (pt0) cc_final: 0.5823 (pt0) REVERT: F 98 LYS cc_start: 0.7082 (tmtt) cc_final: 0.6865 (tptp) REVERT: G 40 GLU cc_start: 0.6110 (pt0) cc_final: 0.5667 (pt0) REVERT: H 40 GLU cc_start: 0.6080 (pt0) cc_final: 0.5744 (pt0) REVERT: B 197 LYS cc_start: 0.7659 (tptp) cc_final: 0.7159 (tppt) REVERT: B 201 ASN cc_start: 0.7662 (m110) cc_final: 0.7279 (m110) REVERT: B 219 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7767 (ttm-80) REVERT: B 224 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7070 (tpp-160) REVERT: B 526 PHE cc_start: 0.6619 (t80) cc_final: 0.6325 (t80) REVERT: B 625 MET cc_start: 0.6812 (ttt) cc_final: 0.6080 (tmm) REVERT: B 669 PHE cc_start: 0.6615 (m-10) cc_final: 0.5873 (t80) REVERT: C 197 LYS cc_start: 0.7613 (tptp) cc_final: 0.7191 (tppt) REVERT: C 201 ASN cc_start: 0.7661 (m110) cc_final: 0.7285 (m110) REVERT: C 219 ARG cc_start: 0.8038 (tpp-160) cc_final: 0.7756 (ttm-80) REVERT: C 224 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7045 (tpp-160) REVERT: C 625 MET cc_start: 0.6873 (ttt) cc_final: 0.6170 (tmm) REVERT: C 669 PHE cc_start: 0.6500 (m-10) cc_final: 0.5895 (t80) REVERT: C 718 MET cc_start: 0.6504 (tpp) cc_final: 0.6140 (tpt) REVERT: C 747 SER cc_start: 0.8537 (m) cc_final: 0.8102 (p) REVERT: D 197 LYS cc_start: 0.7657 (tptp) cc_final: 0.7101 (tppt) REVERT: D 201 ASN cc_start: 0.7686 (m110) cc_final: 0.7311 (m110) REVERT: D 219 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7727 (ttm-80) REVERT: D 224 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7048 (tpp-160) REVERT: D 625 MET cc_start: 0.6948 (ttt) cc_final: 0.6167 (tmm) REVERT: D 747 SER cc_start: 0.8453 (m) cc_final: 0.8042 (p) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.7143 time to fit residues: 611.2182 Evaluate side-chains 433 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 297 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 447 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 447 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26236 Z= 0.275 Angle : 0.587 5.753 35720 Z= 0.310 Chirality : 0.039 0.139 4104 Planarity : 0.005 0.054 4480 Dihedral : 9.476 163.131 3788 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.03 % Allowed : 8.69 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3260 helix: 1.13 (0.12), residues: 1716 sheet: -0.73 (0.30), residues: 260 loop : -0.97 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 409 HIS 0.007 0.001 HIS C 252 PHE 0.016 0.001 PHE C 341 TYR 0.015 0.001 TYR D 236 ARG 0.007 0.001 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 470 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 443 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6850 (tpp-160) REVERT: A 532 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5548 (tt) REVERT: A 583 VAL cc_start: 0.7140 (t) cc_final: 0.6922 (p) REVERT: A 669 PHE cc_start: 0.6793 (m-10) cc_final: 0.5913 (t80) REVERT: E 18 LYS cc_start: 0.5642 (mtpp) cc_final: 0.5429 (mtpp) REVERT: E 40 GLU cc_start: 0.6111 (pt0) cc_final: 0.5885 (pt0) REVERT: E 70 ARG cc_start: 0.6628 (ttm170) cc_final: 0.6252 (ttp-170) REVERT: E 98 LYS cc_start: 0.7217 (tmtt) cc_final: 0.6886 (tptp) REVERT: E 102 GLU cc_start: 0.6301 (tt0) cc_final: 0.5975 (tt0) REVERT: F 165 ASP cc_start: 0.5222 (p0) cc_final: 0.4653 (m-30) REVERT: G 18 LYS cc_start: 0.5614 (mtmm) cc_final: 0.5390 (mtpp) REVERT: G 40 GLU cc_start: 0.5977 (pt0) cc_final: 0.5754 (pt0) REVERT: H 70 ARG cc_start: 0.6568 (ttm170) cc_final: 0.6249 (ttp-170) REVERT: H 182 ARG cc_start: 0.6569 (mtm180) cc_final: 0.5688 (mpp80) REVERT: B 224 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7014 (tpp-160) REVERT: B 625 MET cc_start: 0.6962 (ttt) cc_final: 0.6202 (tmm) REVERT: B 669 PHE cc_start: 0.6698 (m-10) cc_final: 0.5979 (t80) REVERT: B 754 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7907 (mtpt) REVERT: C 224 ARG cc_start: 0.7419 (ttp80) cc_final: 0.6885 (tpp-160) REVERT: C 532 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5383 (tt) REVERT: C 625 MET cc_start: 0.6942 (ttt) cc_final: 0.6231 (tmm) REVERT: C 669 PHE cc_start: 0.6502 (m-10) cc_final: 0.5876 (t80) REVERT: C 718 MET cc_start: 0.6399 (tpp) cc_final: 0.6095 (tmm) REVERT: C 754 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7869 (mtpt) REVERT: D 224 ARG cc_start: 0.7457 (ttp80) cc_final: 0.6888 (tpp-160) REVERT: D 532 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5394 (tt) REVERT: D 625 MET cc_start: 0.7047 (ttt) cc_final: 0.6232 (tmm) REVERT: D 669 PHE cc_start: 0.6543 (m-10) cc_final: 0.5894 (t80) outliers start: 27 outliers final: 23 residues processed: 453 average time/residue: 0.8006 time to fit residues: 551.4499 Evaluate side-chains 445 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 419 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 247 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 295 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26236 Z= 0.234 Angle : 0.556 5.813 35720 Z= 0.287 Chirality : 0.038 0.178 4104 Planarity : 0.004 0.049 4480 Dihedral : 9.142 157.336 3788 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.56 % Allowed : 10.40 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3260 helix: 1.25 (0.12), residues: 1728 sheet: -0.71 (0.30), residues: 264 loop : -0.98 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 409 HIS 0.004 0.001 HIS D 326 PHE 0.014 0.001 PHE C 341 TYR 0.014 0.001 TYR C 236 ARG 0.005 0.001 ARG C 746 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 439 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6781 (tpp-160) REVERT: A 532 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5529 (tt) REVERT: A 625 MET cc_start: 0.6967 (ttm) cc_final: 0.6163 (tmm) REVERT: A 669 PHE cc_start: 0.6585 (m-10) cc_final: 0.5730 (t80) REVERT: E 70 ARG cc_start: 0.6553 (ttm170) cc_final: 0.6194 (ttp-170) REVERT: E 98 LYS cc_start: 0.7186 (tmtt) cc_final: 0.6911 (tptp) REVERT: E 102 GLU cc_start: 0.6254 (tt0) cc_final: 0.5925 (tt0) REVERT: F 165 ASP cc_start: 0.5059 (p0) cc_final: 0.4558 (m-30) REVERT: G 18 LYS cc_start: 0.5653 (mtmm) cc_final: 0.5309 (mtpp) REVERT: G 40 GLU cc_start: 0.6099 (pt0) cc_final: 0.5893 (pt0) REVERT: G 70 ARG cc_start: 0.6454 (ttm170) cc_final: 0.6166 (ttp-170) REVERT: G 165 ASP cc_start: 0.4848 (p0) cc_final: 0.4491 (m-30) REVERT: G 182 ARG cc_start: 0.6621 (mtm180) cc_final: 0.5668 (mpp80) REVERT: H 182 ARG cc_start: 0.6755 (mtm180) cc_final: 0.5828 (mpp80) REVERT: B 224 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6857 (tpp-160) REVERT: B 532 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5429 (tt) REVERT: B 625 MET cc_start: 0.7063 (ttt) cc_final: 0.6260 (tmm) REVERT: B 669 PHE cc_start: 0.6804 (m-10) cc_final: 0.6042 (t80) REVERT: B 754 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7917 (mtpt) REVERT: C 224 ARG cc_start: 0.7341 (ttp80) cc_final: 0.6855 (tpp-160) REVERT: C 532 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5396 (tt) REVERT: C 625 MET cc_start: 0.6999 (ttt) cc_final: 0.6324 (tmm) REVERT: C 669 PHE cc_start: 0.6711 (m-10) cc_final: 0.5998 (t80) REVERT: C 754 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7965 (mtpt) REVERT: D 224 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6842 (tpp-160) REVERT: D 532 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5386 (tt) REVERT: D 625 MET cc_start: 0.7062 (ttt) cc_final: 0.6303 (tmm) REVERT: D 669 PHE cc_start: 0.6702 (m-10) cc_final: 0.5991 (t80) REVERT: D 718 MET cc_start: 0.6495 (tpp) cc_final: 0.5835 (tmm) outliers start: 41 outliers final: 36 residues processed: 455 average time/residue: 0.7902 time to fit residues: 546.2052 Evaluate side-chains 455 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 415 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26236 Z= 0.197 Angle : 0.533 7.354 35720 Z= 0.273 Chirality : 0.037 0.128 4104 Planarity : 0.004 0.046 4480 Dihedral : 9.054 157.650 3788 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.18 % Allowed : 11.62 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3260 helix: 1.36 (0.12), residues: 1732 sheet: -0.78 (0.30), residues: 264 loop : -0.93 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 733 HIS 0.004 0.001 HIS A 326 PHE 0.015 0.001 PHE D 357 TYR 0.011 0.001 TYR C 236 ARG 0.005 0.000 ARG D 746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 435 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6970 (ttp80) cc_final: 0.6565 (tpp-160) REVERT: A 531 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6331 (t70) REVERT: A 532 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5531 (tt) REVERT: A 625 MET cc_start: 0.6946 (ttm) cc_final: 0.6174 (tmm) REVERT: A 669 PHE cc_start: 0.6785 (m-10) cc_final: 0.5789 (t80) REVERT: E 70 ARG cc_start: 0.6600 (ttm170) cc_final: 0.6205 (ttp-170) REVERT: E 98 LYS cc_start: 0.7209 (tmtt) cc_final: 0.6935 (tptp) REVERT: E 102 GLU cc_start: 0.6179 (tt0) cc_final: 0.5889 (tt0) REVERT: G 18 LYS cc_start: 0.5689 (mtmm) cc_final: 0.5285 (mtpp) REVERT: G 70 ARG cc_start: 0.6516 (ttm170) cc_final: 0.6147 (ttp-170) REVERT: G 182 ARG cc_start: 0.6630 (mtm180) cc_final: 0.5724 (mpp80) REVERT: H 70 ARG cc_start: 0.6509 (ttm170) cc_final: 0.6201 (ttp-170) REVERT: H 182 ARG cc_start: 0.6719 (mtm180) cc_final: 0.5942 (mpp80) REVERT: B 224 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6852 (tpp-160) REVERT: B 526 PHE cc_start: 0.6728 (t80) cc_final: 0.6334 (t80) REVERT: B 532 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5441 (tt) REVERT: B 625 MET cc_start: 0.7082 (ttt) cc_final: 0.6296 (tmm) REVERT: B 669 PHE cc_start: 0.6863 (m-10) cc_final: 0.5995 (t80) REVERT: B 718 MET cc_start: 0.6877 (tpp) cc_final: 0.6606 (tpt) REVERT: B 754 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7937 (mtpt) REVERT: C 224 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6647 (tpp-160) REVERT: C 532 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.5256 (tt) REVERT: C 625 MET cc_start: 0.6954 (ttt) cc_final: 0.6260 (tmm) REVERT: C 669 PHE cc_start: 0.6798 (m-10) cc_final: 0.6004 (t80) REVERT: C 754 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7714 (mtpt) REVERT: D 224 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6627 (tpp-160) REVERT: D 532 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5414 (tt) REVERT: D 625 MET cc_start: 0.7138 (ttt) cc_final: 0.6369 (tmm) REVERT: D 669 PHE cc_start: 0.6646 (m-10) cc_final: 0.5868 (t80) REVERT: D 718 MET cc_start: 0.6161 (tpp) cc_final: 0.5566 (tmm) REVERT: D 754 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7759 (mtpt) outliers start: 31 outliers final: 24 residues processed: 441 average time/residue: 0.7789 time to fit residues: 518.2856 Evaluate side-chains 445 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 416 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 284 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN H 180 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26236 Z= 0.246 Angle : 0.543 6.319 35720 Z= 0.279 Chirality : 0.038 0.157 4104 Planarity : 0.004 0.047 4480 Dihedral : 9.020 157.513 3788 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.60 % Allowed : 12.20 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3260 helix: 1.36 (0.12), residues: 1732 sheet: -0.63 (0.30), residues: 264 loop : -0.99 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 409 HIS 0.005 0.001 HIS B 326 PHE 0.020 0.001 PHE C 357 TYR 0.010 0.001 TYR A 235 ARG 0.006 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 429 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7044 (ttp80) cc_final: 0.6695 (tpp-160) REVERT: A 531 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6411 (t70) REVERT: A 532 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5525 (tt) REVERT: A 625 MET cc_start: 0.7038 (ttm) cc_final: 0.6311 (tmm) REVERT: A 669 PHE cc_start: 0.6777 (m-10) cc_final: 0.5771 (t80) REVERT: E 70 ARG cc_start: 0.6625 (ttm170) cc_final: 0.6227 (ttp-170) REVERT: E 98 LYS cc_start: 0.7198 (tmtt) cc_final: 0.6896 (tptp) REVERT: E 102 GLU cc_start: 0.6182 (tt0) cc_final: 0.5880 (tt0) REVERT: F 165 ASP cc_start: 0.4709 (p0) cc_final: 0.4375 (m-30) REVERT: G 165 ASP cc_start: 0.4759 (p0) cc_final: 0.4302 (m-30) REVERT: G 182 ARG cc_start: 0.6615 (mtm180) cc_final: 0.5784 (mpp80) REVERT: H 182 ARG cc_start: 0.6682 (mtm180) cc_final: 0.5891 (mpp80) REVERT: B 224 ARG cc_start: 0.6982 (ttp80) cc_final: 0.6665 (tpp-160) REVERT: B 526 PHE cc_start: 0.6652 (t80) cc_final: 0.6280 (t80) REVERT: B 532 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5424 (tt) REVERT: B 625 MET cc_start: 0.7121 (ttt) cc_final: 0.6331 (tmm) REVERT: B 669 PHE cc_start: 0.6916 (m-10) cc_final: 0.6052 (t80) REVERT: B 718 MET cc_start: 0.6710 (tpp) cc_final: 0.6455 (tpt) REVERT: B 754 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7767 (mtpt) REVERT: C 187 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6216 (mt-10) REVERT: C 224 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6640 (tpp-160) REVERT: C 532 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5229 (tt) REVERT: C 625 MET cc_start: 0.7090 (ttt) cc_final: 0.6388 (tmm) REVERT: C 669 PHE cc_start: 0.6864 (m-10) cc_final: 0.5981 (t80) REVERT: C 754 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7711 (mtpt) REVERT: D 224 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6643 (tpp-160) REVERT: D 532 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5263 (tt) REVERT: D 625 MET cc_start: 0.7079 (ttt) cc_final: 0.6355 (tmm) REVERT: D 669 PHE cc_start: 0.6765 (m-10) cc_final: 0.5928 (t80) REVERT: D 754 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7813 (mtpt) outliers start: 42 outliers final: 29 residues processed: 442 average time/residue: 0.7671 time to fit residues: 514.8070 Evaluate side-chains 452 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 418 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 317 optimal weight: 0.0970 chunk 263 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26236 Z= 0.198 Angle : 0.526 6.051 35720 Z= 0.267 Chirality : 0.037 0.129 4104 Planarity : 0.004 0.049 4480 Dihedral : 8.959 157.438 3788 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.45 % Allowed : 12.80 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3260 helix: 1.47 (0.12), residues: 1728 sheet: -0.55 (0.30), residues: 264 loop : -0.87 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 733 HIS 0.004 0.001 HIS A 326 PHE 0.026 0.001 PHE A 519 TYR 0.009 0.001 TYR C 236 ARG 0.006 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 426 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6638 (tpp-160) REVERT: A 531 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6375 (t70) REVERT: A 532 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5593 (tt) REVERT: A 625 MET cc_start: 0.7255 (ttm) cc_final: 0.6309 (tmm) REVERT: A 669 PHE cc_start: 0.6872 (m-10) cc_final: 0.5823 (t80) REVERT: E 70 ARG cc_start: 0.6646 (ttm170) cc_final: 0.6287 (ttp-170) REVERT: E 98 LYS cc_start: 0.7167 (tmtt) cc_final: 0.6855 (tptp) REVERT: E 102 GLU cc_start: 0.6251 (tt0) cc_final: 0.5943 (tt0) REVERT: F 159 CYS cc_start: 0.7324 (m) cc_final: 0.7112 (m) REVERT: F 165 ASP cc_start: 0.4559 (p0) cc_final: 0.4318 (m-30) REVERT: G 182 ARG cc_start: 0.6470 (mtm180) cc_final: 0.5780 (mtt-85) REVERT: H 182 ARG cc_start: 0.6598 (mtm180) cc_final: 0.5934 (mtt-85) REVERT: B 224 ARG cc_start: 0.6965 (ttp80) cc_final: 0.6658 (tpp-160) REVERT: B 526 PHE cc_start: 0.6621 (t80) cc_final: 0.6342 (t80) REVERT: B 532 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5465 (tt) REVERT: B 625 MET cc_start: 0.7138 (ttt) cc_final: 0.6323 (tmm) REVERT: B 669 PHE cc_start: 0.6915 (m-10) cc_final: 0.6050 (t80) REVERT: B 754 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7763 (mtpt) REVERT: C 224 ARG cc_start: 0.7071 (ttp80) cc_final: 0.6595 (tpp-160) REVERT: C 532 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5222 (tt) REVERT: C 624 PHE cc_start: 0.6090 (m-80) cc_final: 0.5807 (m-80) REVERT: C 625 MET cc_start: 0.7077 (ttt) cc_final: 0.6392 (tmm) REVERT: C 669 PHE cc_start: 0.6822 (m-10) cc_final: 0.5981 (t80) REVERT: C 754 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7817 (mtpt) REVERT: D 224 ARG cc_start: 0.7075 (ttp80) cc_final: 0.6630 (tpp-160) REVERT: D 532 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5274 (tt) REVERT: D 625 MET cc_start: 0.7102 (ttt) cc_final: 0.6430 (tmm) REVERT: D 669 PHE cc_start: 0.6793 (m-10) cc_final: 0.5889 (t80) outliers start: 38 outliers final: 27 residues processed: 437 average time/residue: 0.7615 time to fit residues: 505.8729 Evaluate side-chains 443 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 411 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 239 GLN B 204 ASN B 239 GLN B 447 HIS B 528 ASN C 204 ASN C 239 GLN C 447 HIS C 528 ASN D 204 ASN D 239 GLN D 447 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 26236 Z= 0.458 Angle : 0.632 7.360 35720 Z= 0.332 Chirality : 0.041 0.174 4104 Planarity : 0.005 0.055 4480 Dihedral : 9.215 158.781 3788 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.36 % Allowed : 12.96 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3260 helix: 1.01 (0.12), residues: 1736 sheet: -0.54 (0.31), residues: 264 loop : -1.34 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 409 HIS 0.011 0.002 HIS B 326 PHE 0.026 0.002 PHE A 341 TYR 0.014 0.002 TYR D 346 ARG 0.007 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 424 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6663 (tpp-160) REVERT: A 532 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5583 (tt) REVERT: A 625 MET cc_start: 0.7281 (ttm) cc_final: 0.6398 (tmm) REVERT: A 669 PHE cc_start: 0.7002 (m-10) cc_final: 0.5857 (t80) REVERT: E 40 GLU cc_start: 0.6389 (pt0) cc_final: 0.5889 (pt0) REVERT: F 182 ARG cc_start: 0.6617 (mtm180) cc_final: 0.5811 (mpp80) REVERT: G 70 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6336 (ttp-170) REVERT: G 182 ARG cc_start: 0.6640 (mtm180) cc_final: 0.5957 (mtt-85) REVERT: H 182 ARG cc_start: 0.6582 (mtm180) cc_final: 0.5947 (mtt-85) REVERT: B 224 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6684 (tpp-160) REVERT: B 491 TYR cc_start: 0.7406 (m-80) cc_final: 0.7042 (m-80) REVERT: B 532 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5438 (tt) REVERT: B 624 PHE cc_start: 0.6129 (m-80) cc_final: 0.5888 (m-80) REVERT: B 625 MET cc_start: 0.7229 (ttt) cc_final: 0.6336 (tmm) REVERT: B 626 ILE cc_start: 0.7446 (tt) cc_final: 0.7101 (tt) REVERT: B 669 PHE cc_start: 0.6814 (m-10) cc_final: 0.5888 (t80) REVERT: C 224 ARG cc_start: 0.7031 (ttp80) cc_final: 0.6607 (tpp-160) REVERT: C 532 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5273 (tt) REVERT: C 624 PHE cc_start: 0.6360 (m-80) cc_final: 0.6159 (m-80) REVERT: C 625 MET cc_start: 0.7234 (ttt) cc_final: 0.6364 (tmm) REVERT: C 626 ILE cc_start: 0.7437 (tt) cc_final: 0.7067 (tt) REVERT: C 669 PHE cc_start: 0.6876 (m-10) cc_final: 0.5829 (t80) REVERT: C 798 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.6017 (t0) REVERT: D 224 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6617 (tpp-160) REVERT: D 532 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5296 (tt) REVERT: D 625 MET cc_start: 0.7241 (ttt) cc_final: 0.6372 (tmm) REVERT: D 626 ILE cc_start: 0.7478 (tt) cc_final: 0.7145 (tt) REVERT: D 754 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7775 (mtpt) REVERT: D 798 ASP cc_start: 0.6176 (OUTLIER) cc_final: 0.5973 (t0) outliers start: 62 outliers final: 40 residues processed: 460 average time/residue: 0.7452 time to fit residues: 524.3703 Evaluate side-chains 451 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 405 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 531 ASP Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 781 ASP Chi-restraints excluded: chain D residue 798 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 215 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS B 447 HIS C 447 HIS D 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26236 Z= 0.152 Angle : 0.531 7.125 35720 Z= 0.268 Chirality : 0.037 0.134 4104 Planarity : 0.003 0.059 4480 Dihedral : 8.957 157.251 3788 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.41 % Allowed : 13.95 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3260 helix: 1.35 (0.12), residues: 1732 sheet: -0.47 (0.31), residues: 264 loop : -0.85 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 733 HIS 0.003 0.001 HIS A 447 PHE 0.017 0.001 PHE A 519 TYR 0.010 0.001 TYR A 235 ARG 0.008 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 419 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.6593 (t70) cc_final: 0.6326 (t70) REVERT: A 532 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5533 (tt) REVERT: A 610 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6877 (mp) REVERT: A 625 MET cc_start: 0.7337 (ttm) cc_final: 0.6445 (tmm) REVERT: A 669 PHE cc_start: 0.7071 (m-10) cc_final: 0.5908 (t80) REVERT: A 754 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7755 (mtpt) REVERT: E 40 GLU cc_start: 0.6391 (pt0) cc_final: 0.5976 (pt0) REVERT: E 182 ARG cc_start: 0.6309 (mtm180) cc_final: 0.5570 (mpp80) REVERT: F 165 ASP cc_start: 0.4831 (p0) cc_final: 0.4431 (m-30) REVERT: F 180 GLN cc_start: 0.3151 (tp-100) cc_final: 0.2754 (tp40) REVERT: F 182 ARG cc_start: 0.6595 (mtm180) cc_final: 0.5839 (mtt-85) REVERT: G 70 ARG cc_start: 0.6712 (ttm170) cc_final: 0.6315 (ttp-170) REVERT: G 182 ARG cc_start: 0.6532 (mtm180) cc_final: 0.5890 (mtt-85) REVERT: H 182 ARG cc_start: 0.6553 (mtm180) cc_final: 0.5946 (mtt-85) REVERT: B 227 ILE cc_start: 0.9055 (mm) cc_final: 0.8825 (mm) REVERT: B 532 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5460 (tt) REVERT: B 624 PHE cc_start: 0.6226 (m-80) cc_final: 0.6018 (m-80) REVERT: B 625 MET cc_start: 0.7155 (ttt) cc_final: 0.6278 (tmm) REVERT: B 626 ILE cc_start: 0.7290 (tt) cc_final: 0.6977 (tt) REVERT: B 669 PHE cc_start: 0.6908 (m-10) cc_final: 0.5833 (t80) REVERT: B 754 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7696 (mmmt) REVERT: C 532 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5305 (tt) REVERT: C 610 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6910 (mp) REVERT: C 625 MET cc_start: 0.7100 (ttt) cc_final: 0.6315 (tmm) REVERT: C 626 ILE cc_start: 0.7220 (tt) cc_final: 0.6893 (tt) REVERT: C 669 PHE cc_start: 0.6911 (m-10) cc_final: 0.5842 (t80) REVERT: D 532 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5283 (tt) REVERT: D 610 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6916 (mp) REVERT: D 625 MET cc_start: 0.7169 (ttt) cc_final: 0.6348 (tmm) REVERT: D 626 ILE cc_start: 0.7259 (tt) cc_final: 0.6917 (tt) REVERT: D 669 PHE cc_start: 0.6946 (m-10) cc_final: 0.5936 (t80) outliers start: 37 outliers final: 25 residues processed: 436 average time/residue: 0.7292 time to fit residues: 491.1911 Evaluate side-chains 434 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 402 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.0670 chunk 302 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 294 optimal weight: 0.4980 chunk 177 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 231 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN B 447 HIS C 447 HIS D 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26236 Z= 0.174 Angle : 0.523 6.832 35720 Z= 0.263 Chirality : 0.037 0.129 4104 Planarity : 0.003 0.054 4480 Dihedral : 8.806 156.201 3788 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.37 % Allowed : 14.41 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3260 helix: 1.49 (0.12), residues: 1744 sheet: -0.39 (0.31), residues: 264 loop : -0.90 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 733 HIS 0.004 0.001 HIS A 326 PHE 0.017 0.001 PHE A 519 TYR 0.008 0.001 TYR C 236 ARG 0.007 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 406 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.6563 (t70) cc_final: 0.6304 (t70) REVERT: A 532 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5588 (tt) REVERT: A 610 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6887 (mp) REVERT: A 625 MET cc_start: 0.7411 (ttm) cc_final: 0.6476 (tmm) REVERT: A 669 PHE cc_start: 0.7054 (m-10) cc_final: 0.5884 (t80) REVERT: E 40 GLU cc_start: 0.6321 (pt0) cc_final: 0.5888 (pt0) REVERT: E 182 ARG cc_start: 0.6315 (mtm180) cc_final: 0.5586 (mpp80) REVERT: F 180 GLN cc_start: 0.3085 (tp-100) cc_final: 0.2649 (tp40) REVERT: F 182 ARG cc_start: 0.6594 (mtm180) cc_final: 0.5845 (mtt-85) REVERT: G 182 ARG cc_start: 0.6568 (mtm180) cc_final: 0.5929 (mtt-85) REVERT: H 180 GLN cc_start: 0.3191 (tp-100) cc_final: 0.2717 (tp40) REVERT: H 182 ARG cc_start: 0.6547 (mtm180) cc_final: 0.5899 (mtt-85) REVERT: B 532 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5458 (tt) REVERT: B 624 PHE cc_start: 0.6306 (m-80) cc_final: 0.6094 (m-80) REVERT: B 625 MET cc_start: 0.7091 (ttt) cc_final: 0.6206 (tmm) REVERT: B 626 ILE cc_start: 0.7292 (tt) cc_final: 0.6971 (tt) REVERT: B 669 PHE cc_start: 0.6925 (m-10) cc_final: 0.5862 (t80) REVERT: B 754 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7708 (mmmt) REVERT: C 532 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5297 (tt) REVERT: C 610 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6889 (mp) REVERT: C 625 MET cc_start: 0.7127 (ttt) cc_final: 0.6265 (tmm) REVERT: C 626 ILE cc_start: 0.7229 (tt) cc_final: 0.6893 (tt) REVERT: C 669 PHE cc_start: 0.6950 (m-10) cc_final: 0.5850 (t80) REVERT: D 532 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5291 (tt) REVERT: D 610 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6912 (mp) REVERT: D 625 MET cc_start: 0.7175 (ttt) cc_final: 0.6345 (tmm) REVERT: D 626 ILE cc_start: 0.7272 (tt) cc_final: 0.6922 (tt) REVERT: D 669 PHE cc_start: 0.6988 (m-10) cc_final: 0.5848 (t80) outliers start: 36 outliers final: 26 residues processed: 423 average time/residue: 0.7209 time to fit residues: 471.3023 Evaluate side-chains 429 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 396 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 0.0270 chunk 311 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 300 optimal weight: 0.6980 chunk 260 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS F 117 ASN B 447 HIS C 447 HIS D 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26236 Z= 0.141 Angle : 0.510 6.743 35720 Z= 0.255 Chirality : 0.036 0.128 4104 Planarity : 0.003 0.061 4480 Dihedral : 8.733 155.756 3788 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.18 % Allowed : 14.56 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3260 helix: 1.66 (0.12), residues: 1744 sheet: -0.28 (0.31), residues: 264 loop : -0.78 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 733 HIS 0.003 0.001 HIS C 326 PHE 0.017 0.001 PHE A 519 TYR 0.008 0.001 TYR B 439 ARG 0.008 0.000 ARG D 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue ILE 113 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 133 is missing expected H atoms. Skipping. Residue MET 134 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue LYS 185 is missing expected H atoms. Skipping. Residue LYS 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue LYS 535 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue LEU 673 is missing expected H atoms. Skipping. Residue LEU 686 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 411 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.6531 (t70) cc_final: 0.6263 (t70) REVERT: A 532 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5582 (tt) REVERT: A 610 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 625 MET cc_start: 0.7395 (ttm) cc_final: 0.6464 (tmm) REVERT: A 626 ILE cc_start: 0.7069 (tt) cc_final: 0.6676 (tt) REVERT: A 669 PHE cc_start: 0.7026 (m-10) cc_final: 0.5859 (t80) REVERT: E 40 GLU cc_start: 0.6391 (pt0) cc_final: 0.5984 (pt0) REVERT: E 182 ARG cc_start: 0.6297 (mtm180) cc_final: 0.5570 (mpp80) REVERT: F 180 GLN cc_start: 0.3088 (tp-100) cc_final: 0.2650 (tp40) REVERT: F 182 ARG cc_start: 0.6580 (mtm180) cc_final: 0.5846 (mtt-85) REVERT: G 182 ARG cc_start: 0.6531 (mtm180) cc_final: 0.5899 (mtt-85) REVERT: H 70 ARG cc_start: 0.6761 (ttm170) cc_final: 0.6183 (ttp-170) REVERT: H 180 GLN cc_start: 0.3195 (tp-100) cc_final: 0.2715 (tp40) REVERT: H 182 ARG cc_start: 0.6549 (mtm180) cc_final: 0.5924 (mtt-85) REVERT: B 453 GLU cc_start: 0.7676 (tp30) cc_final: 0.7385 (tp30) REVERT: B 531 ASP cc_start: 0.6515 (t70) cc_final: 0.6275 (t70) REVERT: B 532 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5472 (tt) REVERT: B 625 MET cc_start: 0.7075 (ttt) cc_final: 0.6205 (tmm) REVERT: B 626 ILE cc_start: 0.7258 (tt) cc_final: 0.6946 (tt) REVERT: B 669 PHE cc_start: 0.6973 (m-10) cc_final: 0.5880 (t80) REVERT: B 754 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7672 (mmmt) REVERT: C 219 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7251 (mpt-90) REVERT: C 453 GLU cc_start: 0.7674 (tp30) cc_final: 0.7376 (tp30) REVERT: C 532 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.5270 (tt) REVERT: C 610 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6856 (mp) REVERT: C 625 MET cc_start: 0.7043 (ttt) cc_final: 0.6221 (tmm) REVERT: C 626 ILE cc_start: 0.7193 (tt) cc_final: 0.6861 (tt) REVERT: C 669 PHE cc_start: 0.6984 (m-10) cc_final: 0.5854 (t80) REVERT: D 532 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5438 (tt) REVERT: D 610 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6903 (mp) REVERT: D 625 MET cc_start: 0.7105 (ttt) cc_final: 0.6249 (tmm) REVERT: D 626 ILE cc_start: 0.7238 (tt) cc_final: 0.6896 (tt) REVERT: D 669 PHE cc_start: 0.7019 (m-10) cc_final: 0.5854 (t80) REVERT: D 718 MET cc_start: 0.5966 (tpp) cc_final: 0.5744 (tmm) outliers start: 31 outliers final: 22 residues processed: 424 average time/residue: 0.7199 time to fit residues: 469.1541 Evaluate side-chains 434 residues out of total 2884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 405 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 697 ILE Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 697 ILE Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.1980 chunk 277 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS B 447 HIS C 447 HIS D 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.209716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189869 restraints weight = 91515.280| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 0.91 r_work: 0.4047 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.3900 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26236 Z= 0.189 Angle : 0.518 6.561 35720 Z= 0.260 Chirality : 0.037 0.129 4104 Planarity : 0.003 0.057 4480 Dihedral : 8.661 156.388 3788 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.26 % Allowed : 14.29 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3260 helix: 1.68 (0.12), residues: 1740 sheet: -0.29 (0.31), residues: 264 loop : -0.85 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.005 0.001 HIS D 326 PHE 0.016 0.001 PHE A 519 TYR 0.008 0.001 TYR C 439 ARG 0.007 0.000 ARG D 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10230.51 seconds wall clock time: 177 minutes 53.46 seconds (10673.46 seconds total)