Starting phenix.real_space_refine on Mon Aug 25 13:58:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkf_34851/08_2025/8hkf_34851.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.048 sd= 0.177 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 16 8.98 5 Zn 4 6.06 5 S 212 5.16 5 C 18588 2.51 5 N 4772 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28700 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 7, ' ZN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 94.964 62.616 128.258 1.00 76.38 S ATOM 4454 SG CYS A 778 98.806 62.321 128.069 1.00 80.73 S ATOM 4508 SG CYS A 785 97.164 65.665 128.995 1.00106.89 S ATOM 11618 SG CYS B 777 85.072 94.976 128.271 1.00 78.75 S ATOM 11624 SG CYS B 778 85.360 98.815 128.069 1.00 81.80 S ATOM 11678 SG CYS B 785 82.006 97.172 128.980 1.00108.36 S ATOM 18788 SG CYS C 777 52.631 85.104 128.346 1.00 76.11 S ATOM 18794 SG CYS C 778 48.797 85.346 128.094 1.00 82.44 S ATOM 18848 SG CYS C 785 50.465 81.992 128.989 1.00106.31 S ATOM 25958 SG CYS D 777 62.645 52.716 128.268 1.00 73.76 S ATOM 25964 SG CYS D 778 62.334 48.877 128.077 1.00 80.93 S ATOM 26018 SG CYS D 785 65.691 50.496 129.000 1.00108.52 S Time building chain proxies: 6.27, per 1000 atoms: 0.22 Number of scatterers: 28700 At special positions: 0 Unit cell: (148.72, 148.72, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 16 19.00 S 212 16.00 O 5108 8.00 N 4772 7.00 C 18588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 778 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 778 " pdb=" ZN C1301 " pdb="ZN ZN C1301 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 778 " pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 785 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 54.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 110 through 137 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.625A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Proline residue: A 221 - end of helix removed outlier: 3.844A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.932A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix removed outlier: 3.506A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.528A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.152A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.804A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 4.117A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.956A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.805A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.751A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 removed outlier: 3.696A pdb=" N ALA B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Proline residue: B 221 - end of helix removed outlier: 3.920A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Proline residue: B 230 - end of helix No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 256 removed outlier: 4.109A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.192A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.621A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.518A pdb=" N ARG B 780 " --> pdb=" O CYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.525A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.813A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 4.124A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.912A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.736A pdb=" N LEU B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.557A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 219 through 228 removed outlier: 3.541A pdb=" N ILE C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 256 removed outlier: 4.127A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.757A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.253A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.701A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 500 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.620A pdb=" N ARG C 780 " --> pdb=" O CYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.538A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.814A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.129A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.957A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 removed outlier: 3.753A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 137 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.818A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 226 through 227 No H-bonds generated for 'chain 'D' and resid 226 through 227' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.067A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.763A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.617A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 500 " --> pdb=" O LYS D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.629A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.507A pdb=" N ARG D 780 " --> pdb=" O CYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.531A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.815A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.135A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.954A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.723A pdb=" N LEU D1017 " --> pdb=" O GLU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.227A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.634A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.085A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.006A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.238A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.101A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.991A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.228A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.112A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.984A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.226A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.636A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.100A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.978A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 3981 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: 5.87 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.15: 1 1.15 - 1.47: 16150 1.47 - 1.78: 12912 1.78 - 2.10: 280 2.10 - 2.41: 1 Bond restraints: 29344 Sorted by residual: bond pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 1.503 0.840 0.663 3.40e-02 8.65e+02 3.80e+02 bond pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " ideal model delta sigma weight residual 1.492 2.412 -0.920 5.00e-02 4.00e+02 3.38e+02 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.336 1.559 -0.223 1.23e-02 6.61e+03 3.29e+02 bond pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 1.520 1.287 0.233 3.00e-02 1.11e+03 6.04e+01 bond pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " ideal model delta sigma weight residual 1.808 1.586 0.222 3.30e-02 9.18e+02 4.55e+01 ... (remaining 29339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.20: 39802 21.20 - 42.41: 9 42.41 - 63.61: 0 63.61 - 84.82: 0 84.82 - 106.02: 1 Bond angle restraints: 39812 Sorted by residual: angle pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO B 139 " pdb=" N PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 112.00 84.71 27.29 1.40e+00 5.10e-01 3.80e+02 angle pdb=" N TRP C 146 " pdb=" CA TRP C 146 " pdb=" C TRP C 146 " ideal model delta sigma weight residual 112.86 134.82 -21.96 1.22e+00 6.72e-01 3.24e+02 angle pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" C TRP D 146 " ideal model delta sigma weight residual 112.86 134.20 -21.34 1.22e+00 6.72e-01 3.06e+02 angle pdb=" C TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta sigma weight residual 111.36 83.74 27.62 1.63e+00 3.76e-01 2.87e+02 ... (remaining 39807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 15898 20.44 - 40.88: 1353 40.88 - 61.32: 283 61.32 - 81.76: 49 81.76 - 102.20: 21 Dihedral angle restraints: 17604 sinusoidal: 6992 harmonic: 10612 Sorted by residual: dihedral pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual 115.10 134.13 -19.03 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" C PRO A 149 " pdb=" N PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual -120.70 -139.50 18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" C TRP D 146 " pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta harmonic sigma weight residual -122.60 -104.45 -18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 17601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4533 0.206 - 0.413: 10 0.413 - 0.619: 2 0.619 - 0.826: 2 0.826 - 1.032: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA PRO A 149 " pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CB PRO A 149 " both_signs ideal model delta sigma weight residual False 2.72 1.69 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA PRO C 149 " pdb=" N PRO C 149 " pdb=" C PRO C 149 " pdb=" CB PRO C 149 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 177 " 0.058 2.00e-02 2.50e+03 4.63e-02 5.35e+01 pdb=" CG TRP C 177 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 177 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 177 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 177 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP C 177 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 177 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 177 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 177 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO C 149 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO D 149 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.074 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 36 2.22 - 2.95: 12769 2.95 - 3.68: 50386 3.68 - 4.41: 86113 4.41 - 5.14: 141623 Nonbonded interactions: 290927 Sorted by model distance: nonbonded pdb=" O TRP C 146 " pdb=" CD1 TRP C 146 " model vdw 1.494 3.260 nonbonded pdb=" O TRP C 146 " pdb=" CG TRP C 146 " model vdw 1.558 3.260 nonbonded pdb=" CD1 LEU B 802 " pdb=" CE1 TYR B 876 " model vdw 1.787 3.760 nonbonded pdb=" O TRP D 146 " pdb=" CG TRP D 146 " model vdw 1.806 3.260 nonbonded pdb=" CD1 LEU D 802 " pdb=" CE1 TYR D 876 " model vdw 1.820 3.760 ... (remaining 290922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 110 through 1304) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.380 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.920 29361 Z= 0.375 Angle : 0.967 106.020 39824 Z= 0.484 Chirality : 0.050 1.032 4548 Planarity : 0.006 0.143 4992 Dihedral : 16.149 102.196 10716 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 0.60 % Allowed : 22.14 % Favored : 77.26 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 3532 helix: -0.01 (0.12), residues: 1684 sheet: -0.37 (0.25), residues: 364 loop : -0.41 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 232 TYR 0.018 0.001 TYR C 403 PHE 0.035 0.002 PHE A 188 TRP 0.094 0.002 TRP C 177 HIS 0.010 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00849 (29344) covalent geometry : angle 0.96744 (39812) hydrogen bonds : bond 0.20551 ( 1416) hydrogen bonds : angle 6.92595 ( 3981) metal coordination : bond 0.00205 ( 16) metal coordination : angle 0.36675 ( 12) Misc. bond : bond 0.41923 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 552 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7781 (ttt90) REVERT: B 168 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 294 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8165 (ttp80) REVERT: B 398 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7714 (ttt90) REVERT: C 950 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7337 (ttp80) REVERT: D 783 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7740 (pttp) REVERT: D 786 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8273 (mppt) REVERT: D 1018 TRP cc_start: 0.8221 (p-90) cc_final: 0.7967 (p-90) outliers start: 19 outliers final: 13 residues processed: 567 average time/residue: 0.5383 time to fit residues: 357.6556 Evaluate side-chains 536 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 522 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 925 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0040 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 298 ASN A 470 GLN A 505 HIS A 535 HIS A 632 ASN A 816 ASN A1175 ASN B 156 ASN B 218 ASN B 270 GLN B 470 GLN B 505 HIS B 535 HIS B 632 ASN B 816 ASN B 845 HIS B1175 ASN C 156 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 357 GLN C 505 HIS C 535 HIS C 632 ASN C 816 ASN C 845 HIS C1175 ASN D 156 ASN D 218 ASN D 251 ASN D 505 HIS D 535 HIS D 614 HIS D 632 ASN D 816 ASN D 845 HIS D1175 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095087 restraints weight = 50048.398| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.08 r_work: 0.3190 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 29361 Z= 0.136 Angle : 0.610 12.501 39824 Z= 0.308 Chirality : 0.043 0.328 4548 Planarity : 0.007 0.282 4992 Dihedral : 4.867 47.202 3921 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 3.02 % Allowed : 20.17 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3532 helix: 0.80 (0.12), residues: 1664 sheet: -0.43 (0.26), residues: 368 loop : 0.06 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1137 TYR 0.019 0.001 TYR A 553 PHE 0.019 0.001 PHE B 188 TRP 0.031 0.001 TRP C 177 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00313 (29344) covalent geometry : angle 0.60982 (39812) hydrogen bonds : bond 0.04593 ( 1416) hydrogen bonds : angle 4.93660 ( 3981) metal coordination : bond 0.00290 ( 16) metal coordination : angle 1.12703 ( 12) Misc. bond : bond 0.00287 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 538 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8494 (p) cc_final: 0.8235 (m) REVERT: A 174 MET cc_start: 0.7300 (tpt) cc_final: 0.6912 (tpp) REVERT: A 200 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.3353 (ttpp) REVERT: A 267 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: A 317 TYR cc_start: 0.8791 (m-80) cc_final: 0.8515 (m-10) REVERT: A 334 MET cc_start: 0.8311 (tpp) cc_final: 0.8046 (mmt) REVERT: A 398 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7828 (ttt90) REVERT: A 788 ASN cc_start: 0.8004 (p0) cc_final: 0.7729 (p0) REVERT: A 791 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7611 (mm-30) REVERT: B 168 LEU cc_start: 0.8067 (tp) cc_final: 0.7805 (tt) REVERT: B 200 LYS cc_start: 0.3252 (OUTLIER) cc_final: 0.3031 (tttt) REVERT: B 398 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7814 (ttt90) REVERT: B 845 HIS cc_start: 0.8056 (m-70) cc_final: 0.7825 (m170) REVERT: C 133 ARG cc_start: 0.7972 (tmm-80) cc_final: 0.7755 (tmm-80) REVERT: C 190 GLU cc_start: 0.7202 (mp0) cc_final: 0.6733 (mp0) REVERT: C 283 PHE cc_start: 0.8732 (t80) cc_final: 0.8516 (t80) REVERT: C 538 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7289 (mmp80) REVERT: C 788 ASN cc_start: 0.8122 (p0) cc_final: 0.7800 (p0) REVERT: C 845 HIS cc_start: 0.7987 (m-70) cc_final: 0.7762 (m170) REVERT: C 1158 LYS cc_start: 0.8289 (mttt) cc_final: 0.8028 (mtmp) REVERT: D 117 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7118 (mm) REVERT: D 192 MET cc_start: 0.6183 (mtp) cc_final: 0.5749 (mtt) REVERT: D 604 LYS cc_start: 0.8010 (pttt) cc_final: 0.7766 (pptt) REVERT: D 782 ASP cc_start: 0.7632 (m-30) cc_final: 0.7362 (m-30) REVERT: D 786 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8292 (mppt) REVERT: D 791 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: D 829 LYS cc_start: 0.7757 (tmtt) cc_final: 0.7499 (tptp) REVERT: D 830 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: D 1202 ASP cc_start: 0.7886 (t70) cc_final: 0.7563 (t0) outliers start: 95 outliers final: 20 residues processed: 589 average time/residue: 0.5595 time to fit residues: 386.7809 Evaluate side-chains 541 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 513 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PRO Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 876 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 114 optimal weight: 0.8980 chunk 347 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 267 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 298 ASN B 632 ASN C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 GLN C 632 ASN D 251 ASN D 470 GLN D 632 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093690 restraints weight = 50469.831| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.15 r_work: 0.3135 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 29361 Z= 0.169 Angle : 0.606 10.148 39824 Z= 0.301 Chirality : 0.044 0.303 4548 Planarity : 0.006 0.153 4992 Dihedral : 5.383 164.661 3909 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 3.81 % Allowed : 19.85 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.14), residues: 3532 helix: 0.94 (0.13), residues: 1692 sheet: -0.32 (0.26), residues: 364 loop : 0.18 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1137 TYR 0.018 0.002 TYR B 403 PHE 0.028 0.002 PHE B 283 TRP 0.040 0.002 TRP C 177 HIS 0.005 0.002 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00417 (29344) covalent geometry : angle 0.60541 (39812) hydrogen bonds : bond 0.04248 ( 1416) hydrogen bonds : angle 4.68649 ( 3981) metal coordination : bond 0.00154 ( 16) metal coordination : angle 0.98104 ( 12) Misc. bond : bond 0.01157 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 551 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8528 (p) cc_final: 0.8203 (m) REVERT: A 200 LYS cc_start: 0.3828 (OUTLIER) cc_final: 0.3562 (ttpp) REVERT: A 317 TYR cc_start: 0.8724 (m-80) cc_final: 0.8483 (m-10) REVERT: A 347 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: A 398 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7956 (ttt90) REVERT: A 538 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7249 (mmp80) REVERT: A 788 ASN cc_start: 0.8051 (p0) cc_final: 0.7769 (p0) REVERT: A 829 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8426 (mmtm) REVERT: A 1158 LYS cc_start: 0.8032 (mtmp) cc_final: 0.7784 (mtmm) REVERT: B 200 LYS cc_start: 0.3339 (OUTLIER) cc_final: 0.3106 (tttt) REVERT: B 350 VAL cc_start: 0.8624 (t) cc_final: 0.8398 (p) REVERT: B 398 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7973 (ttt180) REVERT: B 538 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7269 (mmp80) REVERT: B 565 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: B 829 LYS cc_start: 0.8542 (mttt) cc_final: 0.8161 (tmtt) REVERT: B 830 GLU cc_start: 0.8566 (mp0) cc_final: 0.8327 (OUTLIER) REVERT: B 1140 LEU cc_start: 0.8061 (tp) cc_final: 0.7834 (tp) REVERT: C 180 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: C 283 PHE cc_start: 0.8701 (t80) cc_final: 0.8453 (t80) REVERT: C 538 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7227 (mmp80) REVERT: C 788 ASN cc_start: 0.8150 (p0) cc_final: 0.7825 (p0) REVERT: C 791 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7683 (mm-30) REVERT: C 829 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8403 (mmpt) REVERT: C 1158 LYS cc_start: 0.8186 (mttt) cc_final: 0.7982 (mtmp) REVERT: D 117 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6972 (mm) REVERT: D 168 LEU cc_start: 0.8114 (tp) cc_final: 0.7758 (tt) REVERT: D 234 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8111 (tp) REVERT: D 538 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7319 (mmp80) REVERT: D 604 LYS cc_start: 0.8087 (pttt) cc_final: 0.7832 (pptt) REVERT: D 786 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8280 (mppt) REVERT: D 791 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: D 830 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8351 (mm-30) outliers start: 120 outliers final: 38 residues processed: 634 average time/residue: 0.5549 time to fit residues: 411.4073 Evaluate side-chains 563 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 513 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 79 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 chunk 162 optimal weight: 0.0020 chunk 91 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS B 632 ASN B 845 HIS C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093299 restraints weight = 50039.573| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.16 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 29361 Z= 0.183 Angle : 0.614 10.985 39824 Z= 0.303 Chirality : 0.044 0.281 4548 Planarity : 0.006 0.145 4992 Dihedral : 5.505 176.124 3909 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.65 % Allowed : 20.52 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.14), residues: 3532 helix: 1.04 (0.12), residues: 1712 sheet: -0.37 (0.27), residues: 364 loop : 0.21 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 232 TYR 0.017 0.002 TYR B 403 PHE 0.018 0.002 PHE A 188 TRP 0.040 0.001 TRP C 177 HIS 0.007 0.002 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00458 (29344) covalent geometry : angle 0.61347 (39812) hydrogen bonds : bond 0.04026 ( 1416) hydrogen bonds : angle 4.60102 ( 3981) metal coordination : bond 0.00163 ( 16) metal coordination : angle 1.06693 ( 12) Misc. bond : bond 0.00328 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 530 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8339 (tp40) cc_final: 0.8137 (tp40) REVERT: A 200 LYS cc_start: 0.3890 (OUTLIER) cc_final: 0.3601 (ttpp) REVERT: A 317 TYR cc_start: 0.8671 (m-80) cc_final: 0.8442 (m-10) REVERT: A 355 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 398 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7931 (ttt90) REVERT: A 426 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8341 (p) REVERT: A 538 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7258 (mmp80) REVERT: A 783 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7293 (pttp) REVERT: A 788 ASN cc_start: 0.8038 (p0) cc_final: 0.7760 (p0) REVERT: A 791 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: A 829 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8393 (mmtm) REVERT: A 862 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 1137 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7052 (mtp-110) REVERT: A 1158 LYS cc_start: 0.8057 (mtmp) cc_final: 0.7790 (mtmm) REVERT: B 398 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8016 (ttt180) REVERT: B 538 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7271 (mmp80) REVERT: B 565 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7657 (ttp-170) REVERT: B 829 LYS cc_start: 0.8701 (mttt) cc_final: 0.8168 (tmtt) REVERT: B 830 GLU cc_start: 0.8541 (mp0) cc_final: 0.8209 (OUTLIER) REVERT: B 1140 LEU cc_start: 0.7981 (tp) cc_final: 0.7671 (tp) REVERT: B 1158 LYS cc_start: 0.8021 (mtmp) cc_final: 0.7797 (mtmm) REVERT: C 190 GLU cc_start: 0.7055 (mp0) cc_final: 0.6520 (mp0) REVERT: C 250 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: C 538 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7379 (mmt90) REVERT: C 788 ASN cc_start: 0.8119 (p0) cc_final: 0.7805 (p0) REVERT: C 791 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7669 (mm-30) REVERT: C 829 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8358 (mmpt) REVERT: C 1140 LEU cc_start: 0.8147 (tp) cc_final: 0.7910 (tp) REVERT: C 1158 LYS cc_start: 0.8203 (mttt) cc_final: 0.7976 (mtmp) REVERT: D 117 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6980 (mm) REVERT: D 168 LEU cc_start: 0.7976 (tp) cc_final: 0.7594 (tt) REVERT: D 169 TRP cc_start: 0.7956 (m100) cc_final: 0.7485 (m100) REVERT: D 234 LEU cc_start: 0.8263 (tp) cc_final: 0.7922 (tp) REVERT: D 538 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7300 (mmp80) REVERT: D 602 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7145 (p0) REVERT: D 604 LYS cc_start: 0.8183 (pttt) cc_final: 0.7847 (pptt) REVERT: D 786 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8308 (mppt) REVERT: D 791 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: D 830 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8377 (mm-30) outliers start: 115 outliers final: 46 residues processed: 599 average time/residue: 0.5451 time to fit residues: 382.2699 Evaluate side-chains 581 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 520 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 255 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 289 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS B 180 GLN B 632 ASN B1147 GLN C 251 ASN C 632 ASN C 845 HIS C1147 GLN D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093383 restraints weight = 50086.060| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.14 r_work: 0.3130 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29361 Z= 0.167 Angle : 0.605 10.212 39824 Z= 0.298 Chirality : 0.043 0.271 4548 Planarity : 0.005 0.140 4992 Dihedral : 5.452 175.059 3909 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.97 % Allowed : 20.65 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.14), residues: 3532 helix: 1.16 (0.13), residues: 1704 sheet: -0.40 (0.27), residues: 364 loop : 0.18 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 948 TYR 0.016 0.002 TYR B1022 PHE 0.034 0.002 PHE C 188 TRP 0.049 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00415 (29344) covalent geometry : angle 0.60516 (39812) hydrogen bonds : bond 0.03850 ( 1416) hydrogen bonds : angle 4.50450 ( 3981) metal coordination : bond 0.00140 ( 16) metal coordination : angle 1.07775 ( 12) Misc. bond : bond 0.00572 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 528 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8333 (tp40) cc_final: 0.7973 (tp40) REVERT: A 200 LYS cc_start: 0.3561 (OUTLIER) cc_final: 0.3309 (ttpp) REVERT: A 334 MET cc_start: 0.8226 (tpp) cc_final: 0.7980 (mmt) REVERT: A 347 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: A 351 TYR cc_start: 0.6913 (t80) cc_final: 0.6627 (t80) REVERT: A 355 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 398 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7909 (ttt90) REVERT: A 426 SER cc_start: 0.8788 (t) cc_final: 0.8346 (p) REVERT: A 538 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7377 (mmt90) REVERT: A 783 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7295 (pttp) REVERT: A 788 ASN cc_start: 0.8083 (p0) cc_final: 0.7821 (p0) REVERT: A 829 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8387 (mmtm) REVERT: A 859 MET cc_start: 0.8689 (ttm) cc_final: 0.8420 (ttm) REVERT: A 892 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6067 (pp20) REVERT: B 398 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8108 (ttt180) REVERT: B 538 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7247 (mmp80) REVERT: B 565 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7587 (ttp-170) REVERT: B 829 LYS cc_start: 0.8666 (mttt) cc_final: 0.8154 (tmtt) REVERT: B 830 GLU cc_start: 0.8504 (mp0) cc_final: 0.8154 (OUTLIER) REVERT: B 1140 LEU cc_start: 0.7984 (tp) cc_final: 0.7737 (tp) REVERT: B 1158 LYS cc_start: 0.7995 (mtmp) cc_final: 0.7764 (mtmm) REVERT: C 170 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8050 (m) REVERT: C 180 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: C 250 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 346 PHE cc_start: 0.7447 (m-10) cc_final: 0.7168 (m-10) REVERT: C 348 GLU cc_start: 0.7888 (tp30) cc_final: 0.7640 (tp30) REVERT: C 382 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8182 (mmtt) REVERT: C 783 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7396 (pttp) REVERT: C 788 ASN cc_start: 0.8177 (p0) cc_final: 0.7867 (p0) REVERT: C 791 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7674 (mm-30) REVERT: C 829 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8342 (mmpt) REVERT: C 876 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: C 1140 LEU cc_start: 0.8102 (tp) cc_final: 0.7761 (tp) REVERT: D 117 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7042 (mm) REVERT: D 200 LYS cc_start: 0.1574 (OUTLIER) cc_final: 0.1202 (mmmt) REVERT: D 308 CYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7978 (m) REVERT: D 382 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8307 (mmtt) REVERT: D 538 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7325 (mmp80) REVERT: D 602 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7150 (p0) REVERT: D 604 LYS cc_start: 0.8127 (pttt) cc_final: 0.7850 (pptt) REVERT: D 791 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: D 830 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (mm-30) outliers start: 125 outliers final: 56 residues processed: 603 average time/residue: 0.5448 time to fit residues: 383.7319 Evaluate side-chains 587 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 511 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 972 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 177 optimal weight: 6.9990 chunk 236 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 254 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS B 632 ASN C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095964 restraints weight = 49491.783| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.23 r_work: 0.3125 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 29361 Z= 0.167 Angle : 0.610 12.687 39824 Z= 0.298 Chirality : 0.043 0.261 4548 Planarity : 0.006 0.135 4992 Dihedral : 5.393 167.882 3909 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 4.26 % Allowed : 20.84 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.14), residues: 3532 helix: 1.23 (0.13), residues: 1692 sheet: -0.43 (0.27), residues: 364 loop : 0.21 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 948 TYR 0.015 0.002 TYR B 403 PHE 0.022 0.002 PHE C 188 TRP 0.056 0.001 TRP C 177 HIS 0.007 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00417 (29344) covalent geometry : angle 0.60999 (39812) hydrogen bonds : bond 0.03792 ( 1416) hydrogen bonds : angle 4.47934 ( 3981) metal coordination : bond 0.00181 ( 16) metal coordination : angle 1.02330 ( 12) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 525 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8389 (p) cc_final: 0.8124 (m) REVERT: A 180 GLN cc_start: 0.8314 (tp40) cc_final: 0.8039 (tp40) REVERT: A 200 LYS cc_start: 0.3709 (OUTLIER) cc_final: 0.3477 (ttpp) REVERT: A 334 MET cc_start: 0.8081 (tpp) cc_final: 0.7841 (mmt) REVERT: A 351 TYR cc_start: 0.6965 (t80) cc_final: 0.6652 (t80) REVERT: A 355 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 398 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7904 (ttt90) REVERT: A 426 SER cc_start: 0.8817 (t) cc_final: 0.8374 (p) REVERT: A 538 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7345 (mmt90) REVERT: A 783 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7300 (pttp) REVERT: A 788 ASN cc_start: 0.8063 (p0) cc_final: 0.7794 (p0) REVERT: A 829 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8348 (mmtm) REVERT: A 892 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6155 (pp20) REVERT: B 168 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7598 (tt) REVERT: B 398 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8087 (ttt180) REVERT: B 538 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7233 (mmp80) REVERT: B 829 LYS cc_start: 0.8668 (mttt) cc_final: 0.8122 (tmtt) REVERT: B 830 GLU cc_start: 0.8482 (mp0) cc_final: 0.8104 (OUTLIER) REVERT: B 1158 LYS cc_start: 0.8031 (mtmp) cc_final: 0.7796 (mtmm) REVERT: C 170 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.7975 (m) REVERT: C 180 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: C 193 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6004 (mt) REVERT: C 224 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7305 (tt) REVERT: C 250 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: C 252 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6237 (mmt) REVERT: C 291 HIS cc_start: 0.8241 (t70) cc_final: 0.7986 (t-90) REVERT: C 346 PHE cc_start: 0.7381 (m-10) cc_final: 0.7092 (m-10) REVERT: C 565 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7516 (ttp-170) REVERT: C 788 ASN cc_start: 0.8189 (p0) cc_final: 0.7880 (p0) REVERT: C 791 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7634 (mm-30) REVERT: C 829 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8320 (mmpt) REVERT: C 1140 LEU cc_start: 0.8050 (tp) cc_final: 0.7718 (tp) REVERT: C 1160 LEU cc_start: 0.8391 (mt) cc_final: 0.8188 (mt) REVERT: D 117 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7040 (mm) REVERT: D 180 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7767 (tp40) REVERT: D 200 LYS cc_start: 0.1562 (OUTLIER) cc_final: 0.1127 (mmmt) REVERT: D 308 CYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7988 (m) REVERT: D 382 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8306 (mmtt) REVERT: D 538 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7318 (mmp80) REVERT: D 602 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7136 (p0) REVERT: D 604 LYS cc_start: 0.8186 (pttt) cc_final: 0.7846 (pptt) REVERT: D 783 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7802 (pptt) outliers start: 134 outliers final: 65 residues processed: 604 average time/residue: 0.5390 time to fit residues: 380.6276 Evaluate side-chains 598 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 514 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 82 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 353 optimal weight: 20.0000 chunk 322 optimal weight: 0.9980 chunk 315 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 178 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 632 ASN B 632 ASN B1147 GLN C 251 ASN C 369 GLN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095925 restraints weight = 49319.242| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.28 r_work: 0.3080 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 29361 Z= 0.237 Angle : 0.670 19.085 39824 Z= 0.327 Chirality : 0.046 0.255 4548 Planarity : 0.006 0.133 4992 Dihedral : 4.815 38.643 3909 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 3.94 % Allowed : 21.38 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.14), residues: 3532 helix: 1.08 (0.12), residues: 1720 sheet: -0.47 (0.27), residues: 364 loop : 0.04 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B1137 TYR 0.018 0.002 TYR B1022 PHE 0.045 0.002 PHE C 188 TRP 0.061 0.002 TRP C 177 HIS 0.008 0.002 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00593 (29344) covalent geometry : angle 0.67016 (39812) hydrogen bonds : bond 0.04157 ( 1416) hydrogen bonds : angle 4.52565 ( 3981) metal coordination : bond 0.00313 ( 16) metal coordination : angle 1.06249 ( 12) Misc. bond : bond 0.01172 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 537 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8387 (p) cc_final: 0.8075 (m) REVERT: A 200 LYS cc_start: 0.3808 (OUTLIER) cc_final: 0.3544 (ttpp) REVERT: A 334 MET cc_start: 0.8146 (tpp) cc_final: 0.7919 (mmt) REVERT: A 382 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8429 (mmtm) REVERT: A 398 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7947 (ttt90) REVERT: A 426 SER cc_start: 0.8821 (t) cc_final: 0.8419 (p) REVERT: A 538 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7372 (mmt90) REVERT: A 565 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8375 (ttt90) REVERT: A 783 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7315 (pttp) REVERT: A 788 ASN cc_start: 0.8036 (p0) cc_final: 0.7776 (p0) REVERT: A 892 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6315 (pp20) REVERT: B 137 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.5966 (p0) REVERT: B 163 ASN cc_start: 0.8330 (m-40) cc_final: 0.7751 (OUTLIER) REVERT: B 538 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7309 (mmp80) REVERT: B 565 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: B 841 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8375 (tptp) REVERT: B 892 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5475 (pp20) REVERT: B 1158 LYS cc_start: 0.8006 (mtmp) cc_final: 0.7771 (mtmm) REVERT: C 170 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.7979 (m) REVERT: C 180 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: C 193 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6034 (mt) REVERT: C 224 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (tt) REVERT: C 250 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: C 283 PHE cc_start: 0.8632 (t80) cc_final: 0.8321 (t80) REVERT: C 346 PHE cc_start: 0.7448 (m-10) cc_final: 0.7177 (m-10) REVERT: C 348 GLU cc_start: 0.7933 (tp30) cc_final: 0.7578 (tp30) REVERT: C 565 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7547 (ttp-170) REVERT: C 788 ASN cc_start: 0.8215 (p0) cc_final: 0.7912 (p0) REVERT: C 791 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7849 (mt-10) REVERT: C 829 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8325 (mmpt) REVERT: C 1140 LEU cc_start: 0.8043 (tp) cc_final: 0.7729 (tp) REVERT: C 1160 LEU cc_start: 0.8417 (mt) cc_final: 0.8199 (mt) REVERT: D 117 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7145 (mm) REVERT: D 180 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7823 (tp40) REVERT: D 283 PHE cc_start: 0.8494 (t80) cc_final: 0.8291 (t80) REVERT: D 308 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8000 (m) REVERT: D 382 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8337 (mmtt) REVERT: D 538 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7338 (mmp80) REVERT: D 604 LYS cc_start: 0.8222 (pttt) cc_final: 0.7860 (pptt) REVERT: D 783 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7801 (pptt) outliers start: 124 outliers final: 68 residues processed: 608 average time/residue: 0.5692 time to fit residues: 404.9177 Evaluate side-chains 617 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 530 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 301 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS B 218 ASN B 241 ASN B 632 ASN B 845 HIS C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097271 restraints weight = 49525.767| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.14 r_work: 0.3131 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 29361 Z= 0.126 Angle : 0.608 17.333 39824 Z= 0.293 Chirality : 0.042 0.245 4548 Planarity : 0.005 0.131 4992 Dihedral : 4.592 35.700 3909 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.52 % Favored : 97.40 % Rotamer: Outliers : 2.67 % Allowed : 22.78 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.14), residues: 3532 helix: 1.36 (0.13), residues: 1680 sheet: -0.37 (0.28), residues: 360 loop : 0.23 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 948 TYR 0.019 0.001 TYR D 553 PHE 0.022 0.001 PHE D 283 TRP 0.048 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00309 (29344) covalent geometry : angle 0.60786 (39812) hydrogen bonds : bond 0.03493 ( 1416) hydrogen bonds : angle 4.42126 ( 3981) metal coordination : bond 0.00195 ( 16) metal coordination : angle 0.95581 ( 12) Misc. bond : bond 0.00985 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 527 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8372 (p) cc_final: 0.8060 (m) REVERT: A 180 GLN cc_start: 0.8290 (tp40) cc_final: 0.8003 (tp40) REVERT: A 200 LYS cc_start: 0.3907 (OUTLIER) cc_final: 0.3603 (ttpp) REVERT: A 334 MET cc_start: 0.8099 (tpp) cc_final: 0.7890 (mmt) REVERT: A 398 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8093 (ttt180) REVERT: A 426 SER cc_start: 0.8766 (t) cc_final: 0.8343 (p) REVERT: A 565 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8292 (ttt90) REVERT: A 783 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7396 (pttp) REVERT: A 788 ASN cc_start: 0.8023 (p0) cc_final: 0.7790 (p0) REVERT: A 829 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8382 (mmtm) REVERT: A 862 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8729 (p) REVERT: A 892 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6303 (pp20) REVERT: B 137 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.5974 (p0) REVERT: B 163 ASN cc_start: 0.8315 (m-40) cc_final: 0.7732 (OUTLIER) REVERT: B 168 LEU cc_start: 0.8069 (tp) cc_final: 0.7798 (tt) REVERT: B 412 MET cc_start: 0.8724 (ttm) cc_final: 0.8486 (ttm) REVERT: B 538 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7297 (mmp80) REVERT: B 565 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: B 829 LYS cc_start: 0.8652 (mttt) cc_final: 0.8190 (tmtt) REVERT: B 892 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5552 (pp20) REVERT: B 1158 LYS cc_start: 0.8062 (mtmp) cc_final: 0.7832 (mtmm) REVERT: C 170 VAL cc_start: 0.8309 (p) cc_final: 0.7889 (m) REVERT: C 180 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: C 193 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6336 (mt) REVERT: C 224 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7313 (tt) REVERT: C 250 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: C 283 PHE cc_start: 0.8702 (t80) cc_final: 0.8408 (t80) REVERT: C 346 PHE cc_start: 0.7438 (m-10) cc_final: 0.7182 (m-10) REVERT: C 348 GLU cc_start: 0.7917 (tp30) cc_final: 0.7551 (tp30) REVERT: C 783 LYS cc_start: 0.7793 (pptt) cc_final: 0.7561 (pptt) REVERT: C 788 ASN cc_start: 0.8134 (p0) cc_final: 0.7835 (p0) REVERT: C 791 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 829 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8332 (mmpt) REVERT: C 1140 LEU cc_start: 0.8056 (tp) cc_final: 0.7739 (tp) REVERT: C 1142 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7156 (mpt-90) REVERT: D 117 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7242 (mm) REVERT: D 169 TRP cc_start: 0.7943 (m100) cc_final: 0.7453 (m100) REVERT: D 180 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: D 192 MET cc_start: 0.6250 (mtp) cc_final: 0.5584 (mpp) REVERT: D 193 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5017 (mt) REVERT: D 200 LYS cc_start: 0.1567 (OUTLIER) cc_final: 0.0948 (mmmt) REVERT: D 308 CYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8036 (m) REVERT: D 354 MET cc_start: 0.7427 (mtp) cc_final: 0.7184 (mtt) REVERT: D 382 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8343 (mmtt) REVERT: D 538 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7355 (mmp80) REVERT: D 565 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8146 (ttt90) REVERT: D 602 ASP cc_start: 0.7571 (m-30) cc_final: 0.7224 (p0) REVERT: D 604 LYS cc_start: 0.8169 (pttt) cc_final: 0.7819 (pptt) REVERT: D 783 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7830 (pptt) outliers start: 84 outliers final: 45 residues processed: 581 average time/residue: 0.5543 time to fit residues: 376.2027 Evaluate side-chains 584 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 521 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 27 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 279 optimal weight: 0.0570 chunk 22 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS B 180 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS C 251 ASN C 369 GLN C 632 ASN C 845 HIS D 251 ASN D 845 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098160 restraints weight = 49605.261| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.28 r_work: 0.3124 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 29361 Z= 0.123 Angle : 0.614 17.219 39824 Z= 0.294 Chirality : 0.042 0.244 4548 Planarity : 0.005 0.130 4992 Dihedral : 4.473 33.907 3909 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 23.35 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.14), residues: 3532 helix: 1.45 (0.13), residues: 1680 sheet: -0.31 (0.28), residues: 360 loop : 0.31 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 948 TYR 0.018 0.001 TYR D 553 PHE 0.035 0.001 PHE C 188 TRP 0.046 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00302 (29344) covalent geometry : angle 0.61401 (39812) hydrogen bonds : bond 0.03436 ( 1416) hydrogen bonds : angle 4.37163 ( 3981) metal coordination : bond 0.00338 ( 16) metal coordination : angle 1.03714 ( 12) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 533 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8284 (tp40) cc_final: 0.7999 (tp40) REVERT: A 200 LYS cc_start: 0.3871 (OUTLIER) cc_final: 0.3559 (ttpp) REVERT: A 312 PHE cc_start: 0.8058 (m-10) cc_final: 0.7718 (m-10) REVERT: A 398 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8093 (ttt180) REVERT: A 426 SER cc_start: 0.8747 (t) cc_final: 0.8324 (p) REVERT: A 788 ASN cc_start: 0.8049 (p0) cc_final: 0.7846 (p0) REVERT: A 829 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8436 (mmtm) REVERT: A 862 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 892 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6295 (pp20) REVERT: B 137 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.5765 (p0) REVERT: B 177 TRP cc_start: 0.7856 (t60) cc_final: 0.7567 (t60) REVERT: B 538 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7289 (mmp80) REVERT: B 829 LYS cc_start: 0.8658 (mttt) cc_final: 0.8115 (tmtt) REVERT: B 830 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8068 (mp0) REVERT: B 892 GLU cc_start: 0.6105 (tm-30) cc_final: 0.5589 (pp20) REVERT: B 1018 TRP cc_start: 0.8263 (p-90) cc_final: 0.7929 (p-90) REVERT: B 1158 LYS cc_start: 0.8039 (mtmp) cc_final: 0.7813 (mtmm) REVERT: C 170 VAL cc_start: 0.8181 (p) cc_final: 0.7762 (m) REVERT: C 180 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: C 224 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7341 (tt) REVERT: C 346 PHE cc_start: 0.7471 (m-10) cc_final: 0.7212 (m-10) REVERT: C 348 GLU cc_start: 0.7930 (tp30) cc_final: 0.7625 (tp30) REVERT: C 783 LYS cc_start: 0.7732 (pptt) cc_final: 0.7521 (pptt) REVERT: C 788 ASN cc_start: 0.8144 (p0) cc_final: 0.7878 (p0) REVERT: C 791 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 829 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8210 (mmpt) REVERT: C 830 GLU cc_start: 0.8553 (mp0) cc_final: 0.8326 (mm-30) REVERT: C 1140 LEU cc_start: 0.7985 (tp) cc_final: 0.7680 (tp) REVERT: C 1160 LEU cc_start: 0.8374 (mt) cc_final: 0.8140 (mt) REVERT: D 117 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7196 (mm) REVERT: D 169 TRP cc_start: 0.7970 (m100) cc_final: 0.7395 (m100) REVERT: D 180 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: D 192 MET cc_start: 0.6236 (mtp) cc_final: 0.5584 (mpp) REVERT: D 193 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.4882 (mt) REVERT: D 308 CYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8044 (m) REVERT: D 382 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8390 (mmtm) REVERT: D 538 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7348 (mmp80) REVERT: D 565 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8120 (ttt90) REVERT: D 602 ASP cc_start: 0.7576 (m-30) cc_final: 0.7298 (p0) REVERT: D 604 LYS cc_start: 0.8226 (pttt) cc_final: 0.7809 (pptt) REVERT: D 783 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7833 (pptt) outliers start: 68 outliers final: 39 residues processed: 578 average time/residue: 0.5325 time to fit residues: 360.2455 Evaluate side-chains 570 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 518 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 153 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.0030 chunk 292 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 HIS A1147 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 845 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097977 restraints weight = 49467.393| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.14 r_work: 0.3129 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 29361 Z= 0.119 Angle : 0.626 17.013 39824 Z= 0.298 Chirality : 0.042 0.239 4548 Planarity : 0.007 0.331 4992 Dihedral : 4.519 56.162 3909 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 23.67 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 3532 helix: 1.44 (0.13), residues: 1696 sheet: -0.28 (0.29), residues: 360 loop : 0.32 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG B1137 TYR 0.018 0.001 TYR D 553 PHE 0.028 0.001 PHE B 283 TRP 0.056 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00295 (29344) covalent geometry : angle 0.62583 (39812) hydrogen bonds : bond 0.03319 ( 1416) hydrogen bonds : angle 4.35147 ( 3981) metal coordination : bond 0.00253 ( 16) metal coordination : angle 0.98589 ( 12) Misc. bond : bond 0.01204 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 522 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8257 (tp40) cc_final: 0.7985 (tp40) REVERT: A 200 LYS cc_start: 0.3942 (OUTLIER) cc_final: 0.3669 (ttpp) REVERT: A 252 MET cc_start: 0.7008 (tpt) cc_final: 0.6802 (mmm) REVERT: A 312 PHE cc_start: 0.8144 (m-10) cc_final: 0.7937 (m-10) REVERT: A 347 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6565 (mm-30) REVERT: A 398 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8110 (ttt180) REVERT: A 426 SER cc_start: 0.8731 (t) cc_final: 0.8301 (p) REVERT: A 829 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8312 (mmtm) REVERT: A 862 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8750 (p) REVERT: A 892 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6276 (pp20) REVERT: A 1158 LYS cc_start: 0.8076 (mtmp) cc_final: 0.7808 (mtmm) REVERT: B 128 LEU cc_start: 0.7823 (tm) cc_final: 0.7622 (tt) REVERT: B 137 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.5929 (p0) REVERT: B 538 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7290 (mmp80) REVERT: B 829 LYS cc_start: 0.8646 (mttt) cc_final: 0.8052 (tmtt) REVERT: B 830 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8092 (mp0) REVERT: B 841 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8381 (tptp) REVERT: B 892 GLU cc_start: 0.6105 (tm-30) cc_final: 0.5641 (pp20) REVERT: B 1158 LYS cc_start: 0.8088 (mtmp) cc_final: 0.7868 (mtmm) REVERT: C 170 VAL cc_start: 0.8291 (p) cc_final: 0.7840 (m) REVERT: C 180 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 224 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7341 (tt) REVERT: C 252 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6340 (mmt) REVERT: C 346 PHE cc_start: 0.7505 (m-10) cc_final: 0.7247 (m-10) REVERT: C 348 GLU cc_start: 0.7967 (tp30) cc_final: 0.7659 (tp30) REVERT: C 788 ASN cc_start: 0.8066 (p0) cc_final: 0.7817 (p0) REVERT: C 791 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 829 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8220 (mmpt) REVERT: C 1140 LEU cc_start: 0.8003 (tp) cc_final: 0.7724 (tp) REVERT: C 1160 LEU cc_start: 0.8391 (mt) cc_final: 0.8174 (mt) REVERT: D 169 TRP cc_start: 0.8006 (m100) cc_final: 0.7483 (m100) REVERT: D 192 MET cc_start: 0.6166 (mtp) cc_final: 0.5581 (mpp) REVERT: D 193 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.4854 (mt) REVERT: D 200 LYS cc_start: 0.1602 (OUTLIER) cc_final: 0.1009 (mmmt) REVERT: D 252 MET cc_start: 0.6970 (tpt) cc_final: 0.6695 (mpt) REVERT: D 283 PHE cc_start: 0.8768 (t80) cc_final: 0.8561 (t80) REVERT: D 308 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8118 (m) REVERT: D 354 MET cc_start: 0.7494 (mtp) cc_final: 0.7236 (mtt) REVERT: D 382 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8406 (mmtm) REVERT: D 538 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7339 (mmp80) REVERT: D 602 ASP cc_start: 0.7583 (m-30) cc_final: 0.7322 (p0) REVERT: D 604 LYS cc_start: 0.8189 (pttt) cc_final: 0.7814 (pptt) REVERT: D 783 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7795 (pptt) outliers start: 59 outliers final: 39 residues processed: 566 average time/residue: 0.5862 time to fit residues: 388.6093 Evaluate side-chains 569 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 516 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 193 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 255 optimal weight: 0.0170 chunk 109 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 347 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 40.0000 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 ASN A 845 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS C 251 ASN C 632 ASN C 845 HIS D 251 ASN D 845 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097465 restraints weight = 49748.418| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29361 Z= 0.129 Angle : 0.632 16.921 39824 Z= 0.299 Chirality : 0.042 0.238 4548 Planarity : 0.005 0.126 4992 Dihedral : 5.269 178.885 3909 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 23.54 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 3532 helix: 1.46 (0.13), residues: 1696 sheet: -0.32 (0.29), residues: 364 loop : 0.33 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 948 TYR 0.016 0.001 TYR D 553 PHE 0.030 0.001 PHE C 188 TRP 0.061 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00320 (29344) covalent geometry : angle 0.63188 (39812) hydrogen bonds : bond 0.03409 ( 1416) hydrogen bonds : angle 4.34626 ( 3981) metal coordination : bond 0.00285 ( 16) metal coordination : angle 1.02739 ( 12) Misc. bond : bond 0.00458 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12699.79 seconds wall clock time: 215 minutes 50.85 seconds (12950.85 seconds total)