Starting phenix.real_space_refine on Mon Aug 25 14:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.map" model { file = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hyj_35086/08_2025/8hyj_35086.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 161 5.16 5 C 17890 2.51 5 N 4986 2.21 5 O 5443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 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: 28568 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8794 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 42, 'TRANS': 1098} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7912 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 40, 'TRANS': 1013} Chain breaks: 10 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 38, 'ASP:plan': 21, 'TRP:plan': 1, 'TYR:plan': 2, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 343 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2123 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1652 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 554 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1417 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 904 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'HIS:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 702 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "J" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 484 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 756 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 309 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 749 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 746 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17355 SG CYS C 90 60.680 84.146 143.944 1.00 95.55 S ATOM 17378 SG CYS C 93 57.920 83.536 141.364 1.00105.96 S ATOM 17419 SG CYS C 99 57.118 84.814 144.844 1.00 80.86 S ATOM 17441 SG CYS C 102 58.791 86.914 141.950 1.00 77.68 S ATOM 24296 SG CYS I 7 45.093 155.861 39.569 1.00 97.61 S ATOM 24312 SG CYS I 10 42.976 153.903 41.222 1.00 99.01 S ATOM 24439 SG CYS I 29 45.564 153.282 37.551 1.00117.62 S ATOM 24458 SG CYS I 32 42.257 154.176 37.378 1.00116.72 S ATOM 25006 SG CYS J 7 63.320 115.605 129.564 1.00 47.84 S ATOM 25030 SG CYS J 10 65.362 115.545 133.098 1.00 51.10 S ATOM 25284 SG CYS J 44 66.199 118.184 130.418 1.00 53.90 S ATOM 25290 SG CYS J 45 63.042 117.973 132.249 1.00 54.08 S ATOM 26226 SG CYS L 12 24.478 99.768 111.775 1.00 72.87 S ATOM 26244 SG CYS L 15 22.009 100.937 114.195 1.00 85.23 S ATOM 26337 SG CYS L 29 21.755 97.770 111.461 1.00 78.65 S ATOM 26353 SG CYS L 32 21.454 100.798 109.987 1.00 84.11 S Time building chain proxies: 6.39, per 1000 atoms: 0.22 Number of scatterers: 28568 At special positions: 0 Unit cell: (146.3, 173.8, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 161 16.00 P 83 15.00 Mg 1 11.99 O 5443 8.00 N 4986 7.00 C 17890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 24 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 39 sheets defined 35.2% alpha, 15.2% beta 21 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.531A pdb=" N THR A 44 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 45 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.911A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.734A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 215 through 219 removed outlier: 4.059A pdb=" N LEU A 218 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 275 removed outlier: 4.040A pdb=" N THR A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.548A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.610A pdb=" N GLN A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 removed outlier: 3.767A pdb=" N SER A 422 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 509 through 519 removed outlier: 4.320A pdb=" N TYR A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 removed outlier: 3.597A pdb=" N ILE A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 4.213A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 616 removed outlier: 3.661A pdb=" N THR A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 606 - end of helix removed outlier: 3.568A pdb=" N ALA A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.580A pdb=" N VAL A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 675 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.718A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 750 through 784 Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 828 through 846 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 862 removed outlier: 3.654A pdb=" N SER A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 3.752A pdb=" N ARG A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 901 removed outlier: 3.651A pdb=" N ARG A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 901 " --> pdb=" O CYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.729A pdb=" N THR A 911 " --> pdb=" O SER A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.828A pdb=" N ASP A 955 " --> pdb=" O ILE A 951 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.875A pdb=" N ARG A 981 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 1014 through 1033 removed outlier: 3.627A pdb=" N GLU A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A1028 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1029 " --> pdb=" O CYS A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 3.514A pdb=" N CYS A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1119 Processing helix chain 'A' and resid 1120 through 1140 removed outlier: 3.549A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1180 through 1188 removed outlier: 3.907A pdb=" N GLU A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 4.018A pdb=" N CYS A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 removed outlier: 4.231A pdb=" N SER A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1225 removed outlier: 3.637A pdb=" N GLY A1224 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1225 " --> pdb=" O GLY A1222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1221 through 1225' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.786A pdb=" N LEU B 26 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.271A pdb=" N CYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 39 " --> pdb=" O CYS B 35 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.922A pdb=" N TYR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.699A pdb=" N ALA B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 304 through 321 removed outlier: 3.589A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.801A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.668A pdb=" N LEU B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.525A pdb=" N GLU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.088A pdb=" N TYR B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.768A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 487 " --> pdb=" O PRO B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 586 through 599 Processing helix chain 'B' and resid 634 through 640 Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.634A pdb=" N GLU B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 670' Processing helix chain 'B' and resid 675 through 682 removed outlier: 3.660A pdb=" N GLU B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.593A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.799A pdb=" N ASP B 710 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 755 through 762 Processing helix chain 'B' and resid 949 through 954 removed outlier: 3.707A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 971 removed outlier: 4.577A pdb=" N LEU B 960 " --> pdb=" O THR B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1008 removed outlier: 3.539A pdb=" N GLN B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B1006 " --> pdb=" O GLU B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1048 removed outlier: 3.968A pdb=" N LYS B1047 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1087 Processing helix chain 'B' and resid 1089 through 1098 Processing helix chain 'B' and resid 1148 through 1162 removed outlier: 3.524A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.607A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.586A pdb=" N ARG C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 4.408A pdb=" N MET C 82 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.767A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.570A pdb=" N THR C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 204' Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 211 through 216 removed outlier: 4.635A pdb=" N GLU C 214 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.828A pdb=" N TYR C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 278 through 294 removed outlier: 3.966A pdb=" N ASN C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.920A pdb=" N VAL D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 removed outlier: 4.279A pdb=" N ARG D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 4.048A pdb=" N VAL D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Proline residue: D 148 - end of helix Processing helix chain 'D' and resid 155 through 166 Processing helix chain 'D' and resid 169 through 177 Processing helix chain 'D' and resid 178 through 181 removed outlier: 4.090A pdb=" N LYS D 181 " --> pdb=" O PRO D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 183 through 201 removed outlier: 6.073A pdb=" N GLN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 22 through 42 removed outlier: 3.756A pdb=" N HIS E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 96 through 111 removed outlier: 3.696A pdb=" N ILE E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'F' and resid 66 through 82 Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.773A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.925A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.847A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.551A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.506A pdb=" N ALA K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 652 No H-bonds generated for 'chain 'W' and resid 650 through 652' Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.906A pdb=" N SER A 323 " --> pdb=" O ARG B1051 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 325 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B1049 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.754A pdb=" N VAL A 400 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS A 401 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 374 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.618A pdb=" N VAL A 797 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 877 through 879 removed outlier: 3.868A pdb=" N ASN A1047 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1227 through 1228 removed outlier: 3.998A pdb=" N ILE F 114 " --> pdb=" O TRP F 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP F 126 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.676A pdb=" N ALA B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 102 removed outlier: 5.332A pdb=" N ALA B 130 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER B 175 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 132 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB5, first strand: chain 'B' and resid 398 through 401 removed outlier: 3.527A pdb=" N GLN B 220 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 239 removed outlier: 3.844A pdb=" N PHE B 248 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 249 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 269 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 277 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 579 through 584 removed outlier: 5.565A pdb=" N TRP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 576 " --> pdb=" O TRP B 580 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 582 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 660 through 663 removed outlier: 3.690A pdb=" N ARG B 629 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 742 through 745 removed outlier: 3.911A pdb=" N LYS B 885 " --> pdb=" O SER B 901 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 903 " --> pdb=" O VAL B 883 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 883 " --> pdb=" O ARG B 903 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL B 905 " --> pdb=" O GLY B 881 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N GLY B 881 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1014 through 1015 removed outlier: 7.063A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 789 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B1031 " --> pdb=" O VAL B 776 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 859 through 861 removed outlier: 3.773A pdb=" N ILE B 861 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC5, first strand: chain 'B' and resid 1114 through 1115 removed outlier: 4.274A pdb=" N HIS B1106 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1145 " --> pdb=" O MET B1105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B1107 " --> pdb=" O VAL B1143 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1143 " --> pdb=" O ILE B1107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.850A pdb=" N GLU C 16 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 104 through 111 removed outlier: 3.595A pdb=" N VAL C 104 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 52 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY C 172 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AC9, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.726A pdb=" N GLN E 161 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N ASP G 56 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N MET G 75 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR G 54 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N SER G 77 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL G 52 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET G 79 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.140A pdb=" N PHE G 76 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP G 9 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 74 " --> pdb=" O TRP G 9 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 13 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL G 70 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 89 through 96 removed outlier: 6.729A pdb=" N PHE G 102 " --> pdb=" O HIS G 94 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL G 96 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY G 100 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL G 101 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR G 112 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET G 103 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASN G 110 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE G 161 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN G 110 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 163 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER G 114 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY G 151 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER G 166 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 149 " --> pdb=" O SER G 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY G 91 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL G 147 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE G 89 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 122 through 124 removed outlier: 3.887A pdb=" N ILE G 130 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 17 removed outlier: 5.667A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 115 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS H 96 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY H 95 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 139 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE H 8 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 14 through 19 Processing sheet with id=AD9, first strand: chain 'I' and resid 84 through 89 removed outlier: 3.788A pdb=" N TRP I 112 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.378A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 625 through 626 Processing sheet with id=AE3, first strand: chain 'W' and resid 638 through 639 985 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 6.80 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4494 1.28 - 1.41: 7309 1.41 - 1.54: 16992 1.54 - 1.68: 221 1.68 - 1.81: 240 Bond restraints: 29256 Sorted by residual: bond pdb=" CA SER B 535 " pdb=" C SER B 535 " ideal model delta sigma weight residual 1.528 1.416 0.112 1.35e-02 5.49e+03 6.89e+01 bond pdb=" CA GLN B 955 " pdb=" C GLN B 955 " ideal model delta sigma weight residual 1.526 1.448 0.078 9.70e-03 1.06e+04 6.46e+01 bond pdb=" CA LYS B 211 " pdb=" C LYS B 211 " ideal model delta sigma weight residual 1.528 1.444 0.084 1.07e-02 8.73e+03 6.15e+01 bond pdb=" CA HIS C 177 " pdb=" C HIS C 177 " ideal model delta sigma weight residual 1.521 1.426 0.095 1.22e-02 6.72e+03 6.04e+01 bond pdb=" C LEU B 406 " pdb=" O LEU B 406 " ideal model delta sigma weight residual 1.236 1.141 0.096 1.25e-02 6.40e+03 5.88e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 38643 3.83 - 7.65: 1116 7.65 - 11.48: 153 11.48 - 15.31: 30 15.31 - 19.14: 9 Bond angle restraints: 39951 Sorted by residual: angle pdb=" N VAL B 634 " pdb=" CA VAL B 634 " pdb=" C VAL B 634 " ideal model delta sigma weight residual 110.42 125.93 -15.51 9.40e-01 1.13e+00 2.72e+02 angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 111.36 126.20 -14.84 1.09e+00 8.42e-01 1.85e+02 angle pdb=" N SER B 730 " pdb=" CA SER B 730 " pdb=" C SER B 730 " ideal model delta sigma weight residual 111.07 125.56 -14.49 1.07e+00 8.73e-01 1.84e+02 angle pdb=" N ASP J 33 " pdb=" CA ASP J 33 " pdb=" C ASP J 33 " ideal model delta sigma weight residual 113.61 95.01 18.60 1.50e+00 4.44e-01 1.54e+02 angle pdb=" N GLY B 72 " pdb=" CA GLY B 72 " pdb=" C GLY B 72 " ideal model delta sigma weight residual 112.31 131.45 -19.14 1.59e+00 3.96e-01 1.45e+02 ... (remaining 39946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 16773 34.45 - 68.89: 669 68.89 - 103.34: 35 103.34 - 137.78: 1 137.78 - 172.23: 8 Dihedral angle restraints: 17486 sinusoidal: 7233 harmonic: 10253 Sorted by residual: dihedral pdb=" CA GLU B 77 " pdb=" C GLU B 77 " pdb=" N PRO B 78 " pdb=" CA PRO B 78 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" C VAL B 778 " pdb=" N VAL B 778 " pdb=" CA VAL B 778 " pdb=" CB VAL B 778 " ideal model delta harmonic sigma weight residual -122.00 -107.75 -14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" C GLN B 974 " pdb=" N GLN B 974 " pdb=" CA GLN B 974 " pdb=" CB GLN B 974 " ideal model delta harmonic sigma weight residual -122.60 -108.96 -13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 17483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4038 0.134 - 0.269: 456 0.269 - 0.403: 115 0.403 - 0.537: 20 0.537 - 0.672: 7 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CA ARG W 627 " pdb=" N ARG W 627 " pdb=" C ARG W 627 " pdb=" CB ARG W 627 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA LYS B 181 " pdb=" N LYS B 181 " pdb=" C LYS B 181 " pdb=" CB LYS B 181 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA GLU C 28 " pdb=" N GLU C 28 " pdb=" C GLU C 28 " pdb=" CB GLU C 28 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.71e+00 ... (remaining 4633 not shown) Planarity restraints: 4805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1030 " -0.026 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C PRO A1030 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO A1030 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL A1031 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.074 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 134 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 522 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 523 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.060 5.00e-02 4.00e+02 ... (remaining 4802 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 2306 2.70 - 3.25: 26972 3.25 - 3.80: 44375 3.80 - 4.35: 55494 4.35 - 4.90: 90323 Nonbonded interactions: 219470 Sorted by model distance: nonbonded pdb=" N ASP J 33 " pdb=" N ALA J 34 " model vdw 2.155 2.560 nonbonded pdb=" O SER A 707 " pdb=" OH TYR A 713 " model vdw 2.198 3.040 nonbonded pdb=" CZ PHE B 116 " pdb=" CB ALA B 121 " model vdw 2.200 3.760 nonbonded pdb=" NH2 ARG A1060 " pdb=" CG GLU E 210 " model vdw 2.200 3.520 nonbonded pdb=" O4 DT N 6 " pdb=" N6 DA T -6 " model vdw 2.211 3.120 ... (remaining 219465 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.050 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.112 29272 Z= 1.102 Angle : 1.524 40.263 39975 Z= 0.996 Chirality : 0.099 0.672 4636 Planarity : 0.007 0.114 4805 Dihedral : 17.343 172.228 10834 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.39 % Allowed : 9.01 % Favored : 88.60 % Cbeta Deviations : 0.96 % 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: -2.61 (0.12), residues: 3465 helix: -1.03 (0.14), residues: 1133 sheet: -1.53 (0.22), residues: 515 loop : -2.28 (0.12), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 629 TYR 0.033 0.002 TYR C 190 PHE 0.044 0.002 PHE C 24 TRP 0.037 0.003 TRP B 119 HIS 0.016 0.002 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.01500 (29256) covalent geometry : angle 1.48340 (39951) hydrogen bonds : bond 0.20977 ( 1011) hydrogen bonds : angle 7.73601 ( 2868) metal coordination : bond 0.01576 ( 16) metal coordination : angle 14.26044 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 388 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ILE cc_start: 0.7885 (pt) cc_final: 0.7497 (tp) REVERT: A 852 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.6152 (m110) REVERT: A 1035 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 658 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.5816 (tp) REVERT: B 740 THR cc_start: 0.6161 (m) cc_final: 0.5838 (p) REVERT: B 902 LEU cc_start: 0.7248 (mp) cc_final: 0.6280 (tp) REVERT: B 1043 MET cc_start: 0.4568 (mtt) cc_final: 0.4266 (mtm) REVERT: B 1097 PHE cc_start: 0.7971 (t80) cc_final: 0.7593 (t80) REVERT: B 1146 TYR cc_start: 0.8627 (m-10) cc_final: 0.8364 (p90) REVERT: D 192 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8829 (pp30) REVERT: F 74 LEU cc_start: 0.9063 (mt) cc_final: 0.8662 (tt) REVERT: F 98 LEU cc_start: 0.8704 (mt) cc_final: 0.8312 (mm) REVERT: F 102 MET cc_start: 0.9220 (tpt) cc_final: 0.8925 (tmm) REVERT: G 30 LEU cc_start: 0.9194 (mm) cc_final: 0.8943 (pp) REVERT: G 178 GLU cc_start: 0.5304 (mt-10) cc_final: 0.4687 (pm20) outliers start: 67 outliers final: 11 residues processed: 444 average time/residue: 0.2215 time to fit residues: 149.3112 Evaluate side-chains 209 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 258 ASN A 391 HIS A 398 GLN A 461 GLN A 490 GLN A 543 GLN A 664 HIS A 947 GLN A1100 HIS ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 54 ASN ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 135 ASN B 204 GLN B 246 ASN B 397 ASN B 427 GLN B 441 HIS ** B 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 GLN B 577 ASN B 688 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN B 768 ASN B 770 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1038 GLN B1057 HIS ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN C 94 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 202 ASN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 GLN E 215 HIS F 84 ASN ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 GLN H 67 ASN H 94 HIS H 137 GLN I 11 ASN I 12 ASN I 31 ASN I 88 GLN J 16 ASN J 61 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN W 612 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.070158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.056225 restraints weight = 384189.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.057149 restraints weight = 270746.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.057792 restraints weight = 210205.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.058280 restraints weight = 174708.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.058644 restraints weight = 151067.256| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 29272 Z= 0.217 Angle : 0.739 16.546 39975 Z= 0.380 Chirality : 0.044 0.192 4636 Planarity : 0.006 0.062 4805 Dihedral : 16.009 178.790 4721 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 0.28 % Allowed : 6.27 % Favored : 93.45 % 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: -2.01 (0.13), residues: 3465 helix: -0.51 (0.15), residues: 1162 sheet: -1.44 (0.21), residues: 554 loop : -1.86 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 42 TYR 0.028 0.002 TYR A1169 PHE 0.022 0.002 PHE B 951 TRP 0.020 0.002 TRP C 180 HIS 0.010 0.002 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00451 (29256) covalent geometry : angle 0.71076 (39951) hydrogen bonds : bond 0.04956 ( 1011) hydrogen bonds : angle 5.37173 ( 2868) metal coordination : bond 0.01420 ( 16) metal coordination : angle 8.24750 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 235 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9214 (pmm) cc_final: 0.8992 (pmm) REVERT: A 543 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: A 724 PHE cc_start: 0.9214 (m-80) cc_final: 0.8842 (m-10) REVERT: B 495 GLN cc_start: 0.7883 (tt0) cc_final: 0.7180 (tm-30) REVERT: B 786 ASP cc_start: 0.7485 (t70) cc_final: 0.7079 (t0) REVERT: B 926 TYR cc_start: 0.8721 (t80) cc_final: 0.8429 (t80) REVERT: C 33 MET cc_start: 0.9474 (tpp) cc_final: 0.9267 (tpp) REVERT: C 201 MET cc_start: 0.9112 (tmm) cc_final: 0.8867 (tmm) REVERT: C 251 MET cc_start: 0.8314 (mtt) cc_final: 0.7745 (mtt) REVERT: F 102 MET cc_start: 0.9291 (tpt) cc_final: 0.9020 (tmm) REVERT: G 138 ARG cc_start: 0.7512 (ptt-90) cc_final: 0.7261 (ptp90) REVERT: G 178 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6949 (pm20) REVERT: K 48 MET cc_start: 0.8269 (mmm) cc_final: 0.7707 (mmm) REVERT: K 67 LEU cc_start: 0.8166 (mp) cc_final: 0.7852 (mp) REVERT: W 627 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7814 (mmm-85) outliers start: 8 outliers final: 0 residues processed: 243 average time/residue: 0.2118 time to fit residues: 81.6137 Evaluate side-chains 168 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.0670 chunk 289 optimal weight: 0.0670 chunk 154 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 173 optimal weight: 0.0970 chunk 255 optimal weight: 50.0000 chunk 287 optimal weight: 20.0000 overall best weight: 1.0458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 86 HIS A 364 GLN A 515 GLN A 546 GLN A1233 GLN B 124 GLN B 414 HIS B 441 HIS B 510 HIS B 513 HIS ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN B1086 HIS B1104 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.071057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.056940 restraints weight = 380412.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.057869 restraints weight = 270484.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.058545 restraints weight = 210672.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.059033 restraints weight = 175190.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.059327 restraints weight = 152436.140| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29272 Z= 0.109 Angle : 0.574 10.704 39975 Z= 0.294 Chirality : 0.040 0.210 4636 Planarity : 0.004 0.064 4805 Dihedral : 15.749 172.372 4721 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % 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: -1.54 (0.14), residues: 3465 helix: -0.04 (0.15), residues: 1171 sheet: -1.26 (0.22), residues: 527 loop : -1.61 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 115 TYR 0.020 0.001 TYR A 163 PHE 0.017 0.001 PHE A 724 TRP 0.012 0.001 TRP B 119 HIS 0.006 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00238 (29256) covalent geometry : angle 0.55688 (39951) hydrogen bonds : bond 0.03377 ( 1011) hydrogen bonds : angle 4.80381 ( 2868) metal coordination : bond 0.00728 ( 16) metal coordination : angle 5.76522 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8411 (mtm) cc_final: 0.8010 (mpp) REVERT: A 491 MET cc_start: 0.6948 (mmm) cc_final: 0.6530 (mmt) REVERT: A 631 MET cc_start: 0.9070 (mmm) cc_final: 0.8765 (mmm) REVERT: A 724 PHE cc_start: 0.9188 (m-80) cc_final: 0.8959 (m-10) REVERT: A 1141 LYS cc_start: 0.8601 (mmpt) cc_final: 0.8393 (mmmt) REVERT: B 495 GLN cc_start: 0.7783 (tt0) cc_final: 0.7132 (tm-30) REVERT: B 557 MET cc_start: 0.7121 (ptm) cc_final: 0.6853 (tmm) REVERT: B 786 ASP cc_start: 0.7789 (t70) cc_final: 0.7376 (t0) REVERT: B 917 MET cc_start: 0.9201 (mmp) cc_final: 0.8898 (mmp) REVERT: B 926 TYR cc_start: 0.8690 (t80) cc_final: 0.8477 (t80) REVERT: C 189 MET cc_start: 0.8739 (ppp) cc_final: 0.8505 (ppp) REVERT: C 201 MET cc_start: 0.8867 (tmm) cc_final: 0.8611 (tmm) REVERT: C 251 MET cc_start: 0.8122 (mtt) cc_final: 0.7484 (mtt) REVERT: F 102 MET cc_start: 0.9270 (tpt) cc_final: 0.8979 (tmm) REVERT: G 178 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7052 (pm20) REVERT: K 48 MET cc_start: 0.8325 (mmm) cc_final: 0.7790 (mmm) REVERT: W 627 ARG cc_start: 0.8099 (ptt180) cc_final: 0.7848 (mmm-85) REVERT: W 638 VAL cc_start: 0.9306 (m) cc_final: 0.8706 (m) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 0.2060 time to fit residues: 73.8818 Evaluate side-chains 166 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 92 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN B 57 ASN B 62 HIS B 441 HIS B 543 GLN ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 280 GLN G 94 HIS H 137 GLN I 80 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.066125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.052563 restraints weight = 389001.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.053348 restraints weight = 280935.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.053925 restraints weight = 221231.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.054329 restraints weight = 185501.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.054568 restraints weight = 162819.103| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 29272 Z= 0.214 Angle : 0.699 12.023 39975 Z= 0.360 Chirality : 0.043 0.228 4636 Planarity : 0.005 0.056 4805 Dihedral : 15.956 175.149 4721 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % 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: -1.47 (0.14), residues: 3465 helix: -0.17 (0.15), residues: 1162 sheet: -1.02 (0.22), residues: 523 loop : -1.49 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 64 TYR 0.019 0.002 TYR A1169 PHE 0.026 0.002 PHE A 724 TRP 0.022 0.002 TRP A1050 HIS 0.009 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00450 (29256) covalent geometry : angle 0.68039 (39951) hydrogen bonds : bond 0.04827 ( 1011) hydrogen bonds : angle 5.01889 ( 2868) metal coordination : bond 0.01433 ( 16) metal coordination : angle 6.59731 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9119 (pmm) cc_final: 0.8844 (pmm) REVERT: A 406 ASP cc_start: 0.9358 (m-30) cc_final: 0.9104 (m-30) REVERT: A 491 MET cc_start: 0.7678 (mmm) cc_final: 0.7376 (mmt) REVERT: A 724 PHE cc_start: 0.9376 (m-80) cc_final: 0.9123 (m-10) REVERT: B 786 ASP cc_start: 0.7893 (t70) cc_final: 0.7583 (t0) REVERT: C 201 MET cc_start: 0.8775 (tmm) cc_final: 0.8472 (tmm) REVERT: C 251 MET cc_start: 0.8152 (mtt) cc_final: 0.7439 (mtt) REVERT: D 93 MET cc_start: 0.3824 (mmp) cc_final: 0.2207 (mtp) REVERT: D 150 LYS cc_start: 0.9011 (pptt) cc_final: 0.8738 (ptpp) REVERT: G 18 MET cc_start: 0.2395 (mmm) cc_final: 0.2064 (mmt) REVERT: G 24 MET cc_start: 0.6657 (tmm) cc_final: 0.5836 (tmm) REVERT: G 178 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6651 (pm20) REVERT: H 41 MET cc_start: 0.8924 (tmm) cc_final: 0.8542 (tmm) REVERT: H 121 MET cc_start: 0.8876 (ttm) cc_final: 0.8418 (ttm) REVERT: K 48 MET cc_start: 0.8473 (mmm) cc_final: 0.7828 (mmm) REVERT: W 616 ILE cc_start: 0.7518 (mp) cc_final: 0.7312 (mp) REVERT: W 647 PHE cc_start: 0.7553 (t80) cc_final: 0.7316 (t80) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.2098 time to fit residues: 65.5843 Evaluate side-chains 148 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 68 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 321 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 263 optimal weight: 0.4980 chunk 348 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 441 HIS B 450 ASN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN B1093 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 229 GLN H 137 GLN I 31 ASN I 50 HIS I 110 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.065545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.052003 restraints weight = 391275.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.052803 restraints weight = 279199.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.053365 restraints weight = 218837.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.053786 restraints weight = 183725.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.054033 restraints weight = 160415.708| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29272 Z= 0.166 Angle : 0.624 10.732 39975 Z= 0.322 Chirality : 0.041 0.235 4636 Planarity : 0.004 0.050 4805 Dihedral : 15.962 173.032 4721 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -1.39 (0.14), residues: 3465 helix: -0.01 (0.15), residues: 1173 sheet: -1.11 (0.23), residues: 498 loop : -1.48 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 713 TYR 0.018 0.001 TYR A 74 PHE 0.027 0.002 PHE B1097 TRP 0.014 0.001 TRP A1050 HIS 0.008 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00358 (29256) covalent geometry : angle 0.60841 (39951) hydrogen bonds : bond 0.03672 ( 1011) hydrogen bonds : angle 4.88081 ( 2868) metal coordination : bond 0.01299 ( 16) metal coordination : angle 5.63204 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8794 (p0) cc_final: 0.8495 (t0) REVERT: A 405 MET cc_start: 0.9191 (pmm) cc_final: 0.8883 (pmm) REVERT: A 470 MET cc_start: 0.8383 (mtp) cc_final: 0.8137 (mpp) REVERT: A 491 MET cc_start: 0.7760 (mmm) cc_final: 0.7226 (mmt) REVERT: A 609 MET cc_start: 0.8902 (tpp) cc_final: 0.8425 (tpp) REVERT: A 724 PHE cc_start: 0.9343 (m-80) cc_final: 0.9101 (m-10) REVERT: B 607 MET cc_start: 0.8204 (mpp) cc_final: 0.8004 (mpp) REVERT: B 786 ASP cc_start: 0.7897 (t70) cc_final: 0.7538 (t0) REVERT: B 917 MET cc_start: 0.9329 (mmp) cc_final: 0.9056 (mmp) REVERT: C 201 MET cc_start: 0.8694 (tmm) cc_final: 0.8456 (tmm) REVERT: C 251 MET cc_start: 0.8246 (mtt) cc_final: 0.7637 (mtt) REVERT: D 93 MET cc_start: 0.3758 (mmp) cc_final: 0.2093 (mtt) REVERT: F 65 MET cc_start: 0.7186 (ttt) cc_final: 0.6557 (tmm) REVERT: G 178 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6879 (pm20) REVERT: H 41 MET cc_start: 0.8795 (tmm) cc_final: 0.8536 (tmm) REVERT: H 121 MET cc_start: 0.8806 (ttm) cc_final: 0.8420 (ttm) REVERT: K 48 MET cc_start: 0.8512 (mmm) cc_final: 0.8032 (mmm) REVERT: W 647 PHE cc_start: 0.7400 (t80) cc_final: 0.7101 (t80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1979 time to fit residues: 60.0973 Evaluate side-chains 144 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 1 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 250 optimal weight: 30.0000 chunk 204 optimal weight: 9.9990 chunk 216 optimal weight: 0.0470 chunk 209 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 321 optimal weight: 8.9990 overall best weight: 7.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.063229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.050211 restraints weight = 413763.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.050957 restraints weight = 294311.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.051496 restraints weight = 230750.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.051812 restraints weight = 193884.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.052133 restraints weight = 171398.797| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 29272 Z= 0.211 Angle : 0.675 11.291 39975 Z= 0.349 Chirality : 0.042 0.243 4636 Planarity : 0.005 0.062 4805 Dihedral : 16.193 173.337 4721 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.25 % Rotamer: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.51 % 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: -1.60 (0.14), residues: 3465 helix: -0.15 (0.15), residues: 1174 sheet: -1.32 (0.22), residues: 518 loop : -1.59 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 64 TYR 0.031 0.002 TYR B1037 PHE 0.031 0.002 PHE B 283 TRP 0.018 0.002 TRP B 280 HIS 0.011 0.002 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00445 (29256) covalent geometry : angle 0.66042 (39951) hydrogen bonds : bond 0.04368 ( 1011) hydrogen bonds : angle 5.13218 ( 2868) metal coordination : bond 0.01417 ( 16) metal coordination : angle 5.75273 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8732 (p0) cc_final: 0.8416 (t0) REVERT: A 405 MET cc_start: 0.9264 (pmm) cc_final: 0.8837 (pmm) REVERT: A 470 MET cc_start: 0.8461 (mtp) cc_final: 0.8205 (mpp) REVERT: A 491 MET cc_start: 0.8221 (mmm) cc_final: 0.7809 (mmt) REVERT: A 631 MET cc_start: 0.9022 (mmm) cc_final: 0.8780 (mmm) REVERT: A 674 MET cc_start: 0.9119 (tpt) cc_final: 0.8886 (tpt) REVERT: A 724 PHE cc_start: 0.9281 (m-80) cc_final: 0.9040 (m-10) REVERT: B 786 ASP cc_start: 0.8161 (t70) cc_final: 0.7830 (t0) REVERT: B 917 MET cc_start: 0.9305 (mmp) cc_final: 0.9089 (mmp) REVERT: C 201 MET cc_start: 0.8653 (tmm) cc_final: 0.8224 (ppp) REVERT: C 251 MET cc_start: 0.8195 (mtt) cc_final: 0.7593 (mtt) REVERT: D 93 MET cc_start: 0.3947 (mmp) cc_final: 0.2312 (mtt) REVERT: F 65 MET cc_start: 0.7560 (ttt) cc_final: 0.6939 (tmm) REVERT: G 24 MET cc_start: 0.6632 (tmm) cc_final: 0.6154 (tmm) REVERT: G 178 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7272 (pm20) REVERT: H 41 MET cc_start: 0.8896 (tmm) cc_final: 0.8419 (tmm) REVERT: H 121 MET cc_start: 0.8933 (ttm) cc_final: 0.8534 (ttm) REVERT: K 48 MET cc_start: 0.8559 (mmm) cc_final: 0.8017 (mmm) REVERT: W 647 PHE cc_start: 0.7135 (t80) cc_final: 0.6795 (t80) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1793 time to fit residues: 53.7658 Evaluate side-chains 141 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 313 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 208 optimal weight: 0.0670 chunk 141 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 302 optimal weight: 30.0000 chunk 312 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 245 optimal weight: 0.0980 overall best weight: 2.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS K 65 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.064206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.050836 restraints weight = 398712.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.051602 restraints weight = 286289.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.052138 restraints weight = 226028.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.052556 restraints weight = 189848.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.052783 restraints weight = 166113.141| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29272 Z= 0.118 Angle : 0.582 11.602 39975 Z= 0.297 Chirality : 0.040 0.229 4636 Planarity : 0.004 0.052 4805 Dihedral : 16.122 174.279 4721 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.14), residues: 3465 helix: 0.17 (0.15), residues: 1174 sheet: -1.06 (0.23), residues: 472 loop : -1.48 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 33 TYR 0.016 0.001 TYR B1037 PHE 0.033 0.001 PHE H 24 TRP 0.012 0.001 TRP B1012 HIS 0.008 0.001 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00262 (29256) covalent geometry : angle 0.56950 (39951) hydrogen bonds : bond 0.03219 ( 1011) hydrogen bonds : angle 4.82158 ( 2868) metal coordination : bond 0.01156 ( 16) metal coordination : angle 4.97873 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8662 (p0) cc_final: 0.8340 (t0) REVERT: A 405 MET cc_start: 0.9240 (pmm) cc_final: 0.8814 (pmm) REVERT: A 406 ASP cc_start: 0.9223 (m-30) cc_final: 0.8789 (m-30) REVERT: A 470 MET cc_start: 0.8415 (mtp) cc_final: 0.8163 (mpp) REVERT: A 491 MET cc_start: 0.8098 (mmm) cc_final: 0.7794 (mmt) REVERT: A 609 MET cc_start: 0.8857 (tpp) cc_final: 0.8587 (tpp) REVERT: A 631 MET cc_start: 0.9037 (mmm) cc_final: 0.8710 (mmm) REVERT: A 674 MET cc_start: 0.9076 (tpt) cc_final: 0.8725 (tpt) REVERT: A 724 PHE cc_start: 0.9285 (m-80) cc_final: 0.9073 (m-10) REVERT: B 223 MET cc_start: 0.7245 (ttt) cc_final: 0.7043 (ttt) REVERT: B 557 MET cc_start: 0.7785 (ptt) cc_final: 0.7108 (ptm) REVERT: B 786 ASP cc_start: 0.8068 (t70) cc_final: 0.7752 (t0) REVERT: B 917 MET cc_start: 0.9330 (mmp) cc_final: 0.9090 (mmp) REVERT: C 201 MET cc_start: 0.8485 (tmm) cc_final: 0.8193 (ppp) REVERT: C 251 MET cc_start: 0.8107 (mtt) cc_final: 0.7493 (mtt) REVERT: D 93 MET cc_start: 0.3053 (mmp) cc_final: 0.1354 (mtt) REVERT: F 65 MET cc_start: 0.7455 (ttt) cc_final: 0.6894 (tmm) REVERT: G 24 MET cc_start: 0.6907 (tmm) cc_final: 0.6317 (tmm) REVERT: G 64 ARG cc_start: 0.8317 (mmp80) cc_final: 0.7981 (mmm160) REVERT: G 178 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7104 (pm20) REVERT: H 41 MET cc_start: 0.8921 (tmm) cc_final: 0.8446 (tmm) REVERT: H 121 MET cc_start: 0.8821 (ttm) cc_final: 0.8226 (tpp) REVERT: K 48 MET cc_start: 0.8513 (mmm) cc_final: 0.8027 (mmm) REVERT: W 647 PHE cc_start: 0.7155 (t80) cc_final: 0.6801 (t80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1828 time to fit residues: 55.8630 Evaluate side-chains 141 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 260 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 16 optimal weight: 40.0000 chunk 303 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 251 optimal weight: 0.9990 chunk 147 optimal weight: 0.0020 chunk 3 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS H 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.063907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.050557 restraints weight = 398921.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.051337 restraints weight = 288174.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.051898 restraints weight = 225703.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.052245 restraints weight = 188459.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.052550 restraints weight = 166075.666| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29272 Z= 0.130 Angle : 0.589 13.195 39975 Z= 0.300 Chirality : 0.041 0.222 4636 Planarity : 0.004 0.051 4805 Dihedral : 16.114 174.050 4721 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.72 % 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: -1.23 (0.14), residues: 3465 helix: 0.27 (0.15), residues: 1169 sheet: -1.12 (0.23), residues: 486 loop : -1.45 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 427 TYR 0.018 0.001 TYR B1037 PHE 0.023 0.001 PHE H 24 TRP 0.010 0.001 TRP B 119 HIS 0.014 0.001 HIS W 653 Details of bonding type rmsd covalent geometry : bond 0.00283 (29256) covalent geometry : angle 0.57922 (39951) hydrogen bonds : bond 0.03353 ( 1011) hydrogen bonds : angle 4.78097 ( 2868) metal coordination : bond 0.00965 ( 16) metal coordination : angle 4.37621 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8663 (p0) cc_final: 0.8365 (t0) REVERT: A 405 MET cc_start: 0.9280 (pmm) cc_final: 0.8877 (pmm) REVERT: A 406 ASP cc_start: 0.9211 (m-30) cc_final: 0.8802 (m-30) REVERT: A 609 MET cc_start: 0.8882 (tpp) cc_final: 0.8551 (tpp) REVERT: A 724 PHE cc_start: 0.9294 (m-80) cc_final: 0.9082 (m-10) REVERT: A 754 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8692 (mm-30) REVERT: A 1161 MET cc_start: 0.7615 (mmp) cc_final: 0.7392 (mmp) REVERT: B 786 ASP cc_start: 0.8093 (t70) cc_final: 0.7819 (t0) REVERT: B 917 MET cc_start: 0.9263 (mmp) cc_final: 0.9037 (mmp) REVERT: B 1026 MET cc_start: 0.8578 (mpp) cc_final: 0.8174 (mpp) REVERT: C 201 MET cc_start: 0.8283 (tmm) cc_final: 0.8016 (ppp) REVERT: C 251 MET cc_start: 0.8107 (mtt) cc_final: 0.7505 (mtt) REVERT: D 93 MET cc_start: 0.3000 (mmp) cc_final: 0.1133 (mtt) REVERT: D 150 LYS cc_start: 0.9125 (pptt) cc_final: 0.8895 (ptpp) REVERT: F 65 MET cc_start: 0.7562 (ttt) cc_final: 0.6996 (tmm) REVERT: F 102 MET cc_start: 0.9437 (mmp) cc_final: 0.9168 (tmm) REVERT: G 18 MET cc_start: 0.4108 (mtp) cc_final: 0.3847 (mtp) REVERT: G 24 MET cc_start: 0.6955 (tmm) cc_final: 0.6581 (tmm) REVERT: G 178 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7035 (pm20) REVERT: H 41 MET cc_start: 0.8944 (tmm) cc_final: 0.8601 (tmm) REVERT: H 121 MET cc_start: 0.8807 (ttm) cc_final: 0.8284 (ttt) REVERT: K 48 MET cc_start: 0.8491 (mmm) cc_final: 0.8032 (mmm) REVERT: W 647 PHE cc_start: 0.6930 (t80) cc_final: 0.6557 (t80) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.1890 time to fit residues: 58.2584 Evaluate side-chains 147 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 146 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 353 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 overall best weight: 5.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.063103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.049993 restraints weight = 404016.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.050747 restraints weight = 290881.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.051262 restraints weight = 229136.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.051586 restraints weight = 193400.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.051903 restraints weight = 170956.202| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29272 Z= 0.155 Angle : 0.608 10.152 39975 Z= 0.314 Chirality : 0.041 0.215 4636 Planarity : 0.004 0.056 4805 Dihedral : 16.184 174.371 4721 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3465 helix: 0.17 (0.15), residues: 1160 sheet: -1.18 (0.23), residues: 482 loop : -1.41 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 184 TYR 0.019 0.001 TYR B1037 PHE 0.023 0.001 PHE H 24 TRP 0.018 0.001 TRP B 229 HIS 0.013 0.001 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00332 (29256) covalent geometry : angle 0.59769 (39951) hydrogen bonds : bond 0.03602 ( 1011) hydrogen bonds : angle 4.88508 ( 2868) metal coordination : bond 0.01073 ( 16) metal coordination : angle 4.50732 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8609 (p0) cc_final: 0.8298 (t0) REVERT: A 405 MET cc_start: 0.9277 (pmm) cc_final: 0.8876 (pmm) REVERT: A 470 MET cc_start: 0.8684 (mtm) cc_final: 0.8252 (mpp) REVERT: A 609 MET cc_start: 0.8924 (tpp) cc_final: 0.8559 (tpp) REVERT: A 626 MET cc_start: 0.5448 (tpp) cc_final: 0.5031 (tpp) REVERT: A 674 MET cc_start: 0.9149 (tpp) cc_final: 0.8608 (tpp) REVERT: B 223 MET cc_start: 0.7785 (tpp) cc_final: 0.7536 (tpp) REVERT: B 557 MET cc_start: 0.7616 (ppp) cc_final: 0.7129 (ppp) REVERT: B 786 ASP cc_start: 0.8074 (t70) cc_final: 0.7800 (t0) REVERT: B 854 MET cc_start: 0.8896 (mmp) cc_final: 0.8678 (mmm) REVERT: B 917 MET cc_start: 0.9276 (mmp) cc_final: 0.9048 (mmp) REVERT: C 201 MET cc_start: 0.8275 (tmm) cc_final: 0.8056 (tmm) REVERT: C 251 MET cc_start: 0.8027 (mtt) cc_final: 0.7414 (mtt) REVERT: D 93 MET cc_start: 0.2777 (mmp) cc_final: 0.1105 (mtt) REVERT: D 150 LYS cc_start: 0.9115 (pptt) cc_final: 0.8899 (ptpp) REVERT: F 65 MET cc_start: 0.7532 (ttt) cc_final: 0.7073 (tmm) REVERT: F 102 MET cc_start: 0.9414 (mmp) cc_final: 0.9181 (tmm) REVERT: G 178 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6972 (pm20) REVERT: H 41 MET cc_start: 0.9134 (tmm) cc_final: 0.8474 (tmm) REVERT: H 93 MET cc_start: 0.7893 (tpt) cc_final: 0.7660 (tpt) REVERT: H 121 MET cc_start: 0.8827 (ttm) cc_final: 0.8163 (ttt) REVERT: K 48 MET cc_start: 0.8495 (mmm) cc_final: 0.8002 (mmm) REVERT: W 647 PHE cc_start: 0.6524 (t80) cc_final: 0.6102 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1826 time to fit residues: 54.5440 Evaluate side-chains 140 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 105 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 17 optimal weight: 0.0040 chunk 77 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 224 optimal weight: 0.1980 chunk 273 optimal weight: 0.2980 chunk 227 optimal weight: 9.9990 overall best weight: 2.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN A 478 GLN ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.063545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.050428 restraints weight = 405342.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.051166 restraints weight = 289417.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.051717 restraints weight = 227888.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.052127 restraints weight = 191638.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.052320 restraints weight = 167395.695| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.7494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29272 Z= 0.117 Angle : 0.577 8.757 39975 Z= 0.296 Chirality : 0.041 0.195 4636 Planarity : 0.004 0.051 4805 Dihedral : 16.134 174.581 4721 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.16 (0.14), residues: 3465 helix: 0.27 (0.15), residues: 1169 sheet: -1.16 (0.24), residues: 467 loop : -1.34 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 184 TYR 0.019 0.001 TYR B1037 PHE 0.023 0.001 PHE H 24 TRP 0.016 0.001 TRP B 229 HIS 0.018 0.001 HIS B 510 Details of bonding type rmsd covalent geometry : bond 0.00255 (29256) covalent geometry : angle 0.56776 (39951) hydrogen bonds : bond 0.03207 ( 1011) hydrogen bonds : angle 4.71579 ( 2868) metal coordination : bond 0.00795 ( 16) metal coordination : angle 4.15262 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6930 Ramachandran restraints generated. 3465 Oldfield, 0 Emsley, 3465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.9209 (pmm) cc_final: 0.8856 (pmm) REVERT: A 406 ASP cc_start: 0.9181 (m-30) cc_final: 0.8779 (m-30) REVERT: A 470 MET cc_start: 0.8664 (mtm) cc_final: 0.8188 (mpp) REVERT: A 518 MET cc_start: 0.7134 (ppp) cc_final: 0.6880 (ppp) REVERT: A 609 MET cc_start: 0.8991 (tpp) cc_final: 0.8695 (tpp) REVERT: A 674 MET cc_start: 0.9142 (tpp) cc_final: 0.8620 (tpp) REVERT: B 223 MET cc_start: 0.7807 (tpp) cc_final: 0.7559 (tpp) REVERT: B 557 MET cc_start: 0.7599 (ppp) cc_final: 0.7141 (ppp) REVERT: C 201 MET cc_start: 0.8192 (tmm) cc_final: 0.7983 (ppp) REVERT: C 251 MET cc_start: 0.8057 (mtt) cc_final: 0.7472 (mtt) REVERT: D 93 MET cc_start: 0.2747 (mmp) cc_final: 0.1099 (mtt) REVERT: F 65 MET cc_start: 0.7463 (ttt) cc_final: 0.7067 (tmm) REVERT: F 102 MET cc_start: 0.9425 (mmp) cc_final: 0.9194 (tmm) REVERT: G 178 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6834 (pm20) REVERT: H 41 MET cc_start: 0.8922 (tmm) cc_final: 0.8624 (tmm) REVERT: H 93 MET cc_start: 0.7997 (tpt) cc_final: 0.7785 (tpt) REVERT: H 121 MET cc_start: 0.8763 (ttm) cc_final: 0.8123 (ttp) REVERT: K 48 MET cc_start: 0.8461 (mmm) cc_final: 0.7997 (mmm) REVERT: W 647 PHE cc_start: 0.6507 (t80) cc_final: 0.6111 (t80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1813 time to fit residues: 53.8382 Evaluate side-chains 141 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 264 optimal weight: 0.5980 chunk 195 optimal weight: 30.0000 chunk 339 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 15 optimal weight: 0.0020 chunk 39 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 overall best weight: 3.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.063326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.050237 restraints weight = 411146.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.051001 restraints weight = 293732.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.051531 restraints weight = 230562.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.051859 restraints weight = 193265.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.052212 restraints weight = 170477.121| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.7614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29272 Z= 0.119 Angle : 0.571 9.175 39975 Z= 0.293 Chirality : 0.040 0.188 4636 Planarity : 0.004 0.049 4805 Dihedral : 16.133 174.432 4721 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.09 (0.14), residues: 3465 helix: 0.35 (0.15), residues: 1166 sheet: -1.13 (0.24), residues: 481 loop : -1.32 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 184 TYR 0.018 0.001 TYR B1037 PHE 0.022 0.001 PHE H 24 TRP 0.016 0.001 TRP B 229 HIS 0.008 0.001 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00261 (29256) covalent geometry : angle 0.56263 (39951) hydrogen bonds : bond 0.03192 ( 1011) hydrogen bonds : angle 4.66862 ( 2868) metal coordination : bond 0.00829 ( 16) metal coordination : angle 4.08141 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.31 seconds wall clock time: 105 minutes 31.17 seconds (6331.17 seconds total)