Starting phenix.real_space_refine on Sun Jul 5 14:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hyj_35086/07_2026/8hyj_35086.map" } 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-dev-6108/lib/python3.11/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: 6.61, per 1000 atoms: 0.23 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.20 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: 6.83 Time building geometry restraints manager: 3.23 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: 38642 3.83 - 7.65: 1116 7.65 - 11.48: 154 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: 16758 34.45 - 68.89: 649 68.89 - 103.34: 34 103.34 - 137.78: 1 137.78 - 172.23: 8 Dihedral angle restraints: 17450 sinusoidal: 7197 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 17447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 4037 0.134 - 0.269: 456 0.269 - 0.403: 115 0.403 - 0.537: 21 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 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= 1.112 Angle : 1.529 40.263 39975 Z= 1.008 Chirality : 0.100 0.672 4636 Planarity : 0.007 0.114 4805 Dihedral : 17.187 172.228 10798 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 are 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/Z covalent geometry : bond 0.01504 / 1.11 (29256) covalent geometry : angle 1.48897 / 1.01 (39951) hydrogen bonds : bond 0.20977 / 13.94 ( 1011) hydrogen bonds : angle 7.73601 / 5.41 ( 2868) metal coordination : bond 0.01576 / 1.16 ( 16) metal coordination : angle 14.26044 / 10.13 ( 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 : 1.025 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: 0.2081 time to fit residues: 142.2110 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 : 1.036 ------------------------------------------------------------------------------- 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... A 25 HIS ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 364 GLN A 391 HIS A 398 GLN A 461 GLN A 483 HIS A 490 GLN A 543 GLN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS A 947 GLN A1100 HIS ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 54 ASN B 57 ASN B 65 GLN B 135 ASN B 204 GLN B 246 ASN B 397 ASN B 414 HIS B 441 HIS B 510 HIS B 513 HIS B 577 ASN B 688 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 768 ASN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1038 GLN B1052 ASN B1057 HIS B1104 GLN B1116 ASN C 94 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 197 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L 47 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.072526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.058121 restraints weight = 364994.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.059120 restraints weight = 259459.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.059826 restraints weight = 200917.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.060315 restraints weight = 166037.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.060617 restraints weight = 144477.025| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29272 Z= 0.228 Angle : 0.754 17.494 39975 Z= 0.393 Chirality : 0.045 0.299 4636 Planarity : 0.006 0.078 4805 Dihedral : 15.605 176.259 4685 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 0.36 % Allowed : 5.27 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 3465 helix: -0.45 (0.15), residues: 1166 sheet: -1.38 (0.21), residues: 577 loop : -1.94 (0.13), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 801 TYR 0.026 0.002 TYR A1169 PHE 0.021 0.002 PHE C 268 TRP 0.019 0.002 TRP B 229 HIS 0.010 0.002 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 (29256) covalent geometry : angle 0.72515 / 0.39 (39951) hydrogen bonds : bond 0.05445 / 3.48 ( 1011) hydrogen bonds : angle 5.50310 / 3.80 ( 2868) metal coordination : bond 0.02857 / 1.96 ( 16) metal coordination : angle 8.44843 / 5.78 ( 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 246 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 1.142 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: A 543 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: A 609 MET cc_start: 0.8035 (tpp) cc_final: 0.7756 (tpp) REVERT: A 724 PHE cc_start: 0.9290 (m-80) cc_final: 0.8963 (m-10) REVERT: B 495 GLN cc_start: 0.7782 (tt0) cc_final: 0.7223 (tm-30) REVERT: B 740 THR cc_start: 0.8908 (m) cc_final: 0.8470 (p) REVERT: B 786 ASP cc_start: 0.7460 (t70) cc_final: 0.7189 (t0) REVERT: C 251 MET cc_start: 0.8185 (mtt) cc_final: 0.7598 (mtt) REVERT: F 102 MET cc_start: 0.9294 (tpt) cc_final: 0.9041 (tmm) REVERT: G 138 ARG cc_start: 0.7769 (ptt-90) cc_final: 0.7472 (ptp90) REVERT: G 172 LEU cc_start: -0.5177 (OUTLIER) cc_final: -0.5645 (tp) REVERT: G 178 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6516 (pm20) REVERT: H 41 MET cc_start: 0.9313 (tmm) cc_final: 0.9045 (tmm) REVERT: H 121 MET cc_start: 0.8871 (ttm) cc_final: 0.8179 (ttp) REVERT: K 48 MET cc_start: 0.8188 (mmm) cc_final: 0.7599 (mmm) REVERT: K 67 LEU cc_start: 0.7998 (mp) cc_final: 0.7648 (mp) outliers start: 10 outliers final: 1 residues processed: 246 average time/residue: 0.1762 time to fit residues: 69.8274 Evaluate side-chains 173 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 6.9990 chunk 289 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 267 optimal weight: 30.0000 chunk 317 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 255 optimal weight: 50.0000 chunk 287 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 546 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN B 770 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 871 HIS B 918 HIS ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN B1156 GLN ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 HIS F 84 ASN H 137 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.071710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.057628 restraints weight = 384777.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.058598 restraints weight = 272217.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.059232 restraints weight = 210718.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.059745 restraints weight = 175002.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.060122 restraints weight = 150939.406| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29272 Z= 0.151 Angle : 0.638 13.463 39975 Z= 0.330 Chirality : 0.043 0.259 4636 Planarity : 0.005 0.074 4805 Dihedral : 15.553 175.631 4685 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 0.14 % Allowed : 3.70 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3465 helix: -0.21 (0.15), residues: 1175 sheet: -1.28 (0.21), residues: 557 loop : -1.68 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 419 TYR 0.030 0.001 TYR A 163 PHE 0.023 0.002 PHE E 175 TRP 0.013 0.002 TRP C 180 HIS 0.018 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (29256) covalent geometry : angle 0.61450 / 0.33 (39951) hydrogen bonds : bond 0.04290 / 2.76 ( 1011) hydrogen bonds : angle 5.12879 / 3.54 ( 2868) metal coordination : bond 0.01160 / 0.74 ( 16) metal coordination : angle 7.02207 / 4.85 ( 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 215 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 1.171 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 502 MET cc_start: 0.9403 (mmm) cc_final: 0.8912 (mpp) REVERT: A 724 PHE cc_start: 0.9162 (m-80) cc_final: 0.8792 (m-10) REVERT: B 375 MET cc_start: 0.9166 (mtm) cc_final: 0.8843 (mtm) REVERT: B 495 GLN cc_start: 0.7868 (tt0) cc_final: 0.7209 (tm-30) REVERT: B 786 ASP cc_start: 0.7578 (t70) cc_final: 0.7324 (t0) REVERT: C 189 MET cc_start: 0.8788 (ppp) cc_final: 0.8573 (ppp) REVERT: C 251 MET cc_start: 0.8197 (mtt) cc_final: 0.7522 (mtt) REVERT: D 150 LYS cc_start: 0.8988 (pttp) cc_final: 0.8728 (mmmt) REVERT: D 159 MET cc_start: -0.6742 (tpt) cc_final: -0.6964 (tpt) REVERT: F 102 MET cc_start: 0.9283 (tpt) cc_final: 0.9047 (tmm) REVERT: G 178 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6895 (pm20) REVERT: H 41 MET cc_start: 0.9386 (tmm) cc_final: 0.9163 (tmm) REVERT: H 121 MET cc_start: 0.8905 (ttm) cc_final: 0.8083 (ttp) REVERT: K 48 MET cc_start: 0.8224 (mmm) cc_final: 0.7653 (mmm) REVERT: K 67 LEU cc_start: 0.8125 (mp) cc_final: 0.7830 (mp) REVERT: W 627 ARG cc_start: 0.8123 (ptt180) cc_final: 0.7869 (mmm-85) outliers start: 4 outliers final: 0 residues processed: 214 average time/residue: 0.1850 time to fit residues: 64.2307 Evaluate side-chains 162 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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: 5.9990 chunk 199 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS A 86 HIS A 216 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 GLN A1233 GLN B 711 HIS ** B 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 12 ASN I 31 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 612 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.070173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.056258 restraints weight = 387478.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.057164 restraints weight = 277077.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.057811 restraints weight = 216973.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.058256 restraints weight = 180380.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.058605 restraints weight = 157280.445| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29272 Z= 0.168 Angle : 0.629 13.345 39975 Z= 0.326 Chirality : 0.042 0.263 4636 Planarity : 0.005 0.094 4805 Dihedral : 15.574 176.379 4685 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3465 helix: -0.03 (0.15), residues: 1175 sheet: -1.31 (0.21), residues: 555 loop : -1.48 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 70 TYR 0.016 0.001 TYR B 442 PHE 0.016 0.001 PHE A1182 TRP 0.033 0.002 TRP A1050 HIS 0.009 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (29256) covalent geometry : angle 0.60788 / 0.32 (39951) hydrogen bonds : bond 0.04080 / 2.63 ( 1011) hydrogen bonds : angle 4.94146 / 3.43 ( 2868) metal coordination : bond 0.01112 / 0.78 ( 16) metal coordination : angle 6.60669 / 4.53 ( 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 204 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.119 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 406 ASP cc_start: 0.9388 (m-30) cc_final: 0.9143 (m-30) REVERT: A 491 MET cc_start: 0.6815 (mmm) cc_final: 0.6288 (mmt) REVERT: A 502 MET cc_start: 0.9414 (mmm) cc_final: 0.8916 (mpp) REVERT: A 631 MET cc_start: 0.9143 (tpt) cc_final: 0.8735 (tpp) REVERT: A 724 PHE cc_start: 0.9212 (m-80) cc_final: 0.8965 (m-10) REVERT: A 754 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 971 LYS cc_start: 0.7974 (mppt) cc_final: 0.7747 (mmmt) REVERT: B 223 MET cc_start: 0.6915 (tpp) cc_final: 0.6664 (tpp) REVERT: B 495 GLN cc_start: 0.7912 (tt0) cc_final: 0.7229 (tm-30) REVERT: B 786 ASP cc_start: 0.7712 (t70) cc_final: 0.7393 (t0) REVERT: B 854 MET cc_start: 0.9278 (mmm) cc_final: 0.8797 (mmm) REVERT: B 917 MET cc_start: 0.9304 (mmp) cc_final: 0.9080 (mmp) REVERT: C 201 MET cc_start: 0.8598 (tmm) cc_final: 0.8200 (tmm) REVERT: C 251 MET cc_start: 0.8052 (mtt) cc_final: 0.7402 (mtt) REVERT: D 150 LYS cc_start: 0.9017 (pttp) cc_final: 0.8784 (mmtt) REVERT: F 102 MET cc_start: 0.9301 (tpt) cc_final: 0.9065 (tmm) REVERT: G 178 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6904 (pm20) REVERT: H 41 MET cc_start: 0.9313 (tmm) cc_final: 0.9023 (tmm) REVERT: H 121 MET cc_start: 0.8936 (ttm) cc_final: 0.8176 (ttp) REVERT: K 48 MET cc_start: 0.8239 (mmm) cc_final: 0.7721 (mmm) REVERT: K 67 LEU cc_start: 0.8121 (mp) cc_final: 0.7833 (mp) REVERT: W 638 VAL cc_start: 0.9328 (m) cc_final: 0.8990 (m) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1977 time to fit residues: 65.2872 Evaluate side-chains 162 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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: 50.0000 chunk 294 optimal weight: 50.0000 chunk 128 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 321 optimal weight: 40.0000 chunk 210 optimal weight: 0.2980 chunk 256 optimal weight: 40.0000 chunk 263 optimal weight: 30.0000 chunk 348 optimal weight: 40.0000 overall best weight: 12.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 ASN ** 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 280 GLN H 42 HIS H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 612 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.065228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.052047 restraints weight = 408539.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.052828 restraints weight = 290585.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.053382 restraints weight = 227579.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.053788 restraints weight = 190424.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.054083 restraints weight = 166731.414| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 29272 Z= 0.344 Angle : 0.909 18.818 39975 Z= 0.468 Chirality : 0.048 0.252 4636 Planarity : 0.007 0.191 4805 Dihedral : 15.980 176.989 4685 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 3465 helix: -0.68 (0.14), residues: 1172 sheet: -1.45 (0.22), residues: 512 loop : -1.73 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 42 TYR 0.036 0.003 TYR E 194 PHE 0.037 0.003 PHE H 40 TRP 0.026 0.003 TRP A1050 HIS 0.037 0.003 HIS W 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.34 (29256) covalent geometry : angle 0.89284 / 0.47 (39951) hydrogen bonds : bond 0.06477 / 4.13 ( 1011) hydrogen bonds : angle 5.60092 / 3.91 ( 2868) metal coordination : bond 0.02373 / 1.80 ( 16) metal coordination : angle 6.97232 / 4.72 ( 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 190 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.098 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 405 MET cc_start: 0.9039 (pmm) cc_final: 0.8782 (pmm) REVERT: A 406 ASP cc_start: 0.9352 (m-30) cc_final: 0.9135 (m-30) REVERT: A 470 MET cc_start: 0.8534 (mtp) cc_final: 0.8311 (mpp) REVERT: A 491 MET cc_start: 0.7588 (mmm) cc_final: 0.7277 (mmt) REVERT: A 724 PHE cc_start: 0.9319 (m-80) cc_final: 0.9042 (m-10) REVERT: B 713 ARG cc_start: 0.9293 (ptt90) cc_final: 0.9076 (ttp80) REVERT: B 786 ASP cc_start: 0.7917 (t70) cc_final: 0.7592 (t0) REVERT: B 930 GLN cc_start: 0.9096 (tt0) cc_final: 0.8841 (pm20) REVERT: B 1026 MET cc_start: 0.8690 (mmp) cc_final: 0.8378 (mmm) REVERT: C 201 MET cc_start: 0.8404 (tmm) cc_final: 0.8167 (tmm) REVERT: C 251 MET cc_start: 0.8372 (mtt) cc_final: 0.7641 (mtt) REVERT: D 150 LYS cc_start: 0.9026 (pttp) cc_final: 0.8729 (mmmt) REVERT: D 152 TYR cc_start: 0.5762 (m-10) cc_final: 0.5414 (t80) REVERT: D 159 MET cc_start: -0.6582 (tpt) cc_final: -0.6820 (tpt) REVERT: F 74 LEU cc_start: 0.9444 (mt) cc_final: 0.9220 (mt) REVERT: F 114 ILE cc_start: 0.8823 (mp) cc_final: 0.8566 (tp) REVERT: G 24 MET cc_start: 0.6361 (tmm) cc_final: 0.5885 (tmm) REVERT: G 178 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6843 (pm20) REVERT: H 41 MET cc_start: 0.8976 (tmm) cc_final: 0.8627 (tmm) REVERT: H 121 MET cc_start: 0.8933 (ttm) cc_final: 0.8576 (tpp) REVERT: I 95 GLU cc_start: 0.6977 (tp30) cc_final: 0.6754 (tp30) REVERT: K 48 MET cc_start: 0.8638 (mmm) cc_final: 0.7933 (mmm) REVERT: W 647 PHE cc_start: 0.7286 (t80) cc_final: 0.7037 (t80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1941 time to fit residues: 59.7731 Evaluate side-chains 153 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 3.9990 chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 321 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS B 718 GLN B 724 GLN ** B 853 ASN ** 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** H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS I 110 HIS ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.066357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.052691 restraints weight = 387652.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.053529 restraints weight = 274070.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.054113 restraints weight = 213718.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.054553 restraints weight = 178847.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.054803 restraints weight = 156080.043| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29272 Z= 0.140 Angle : 0.639 10.976 39975 Z= 0.328 Chirality : 0.043 0.283 4636 Planarity : 0.005 0.064 4805 Dihedral : 15.811 174.745 4685 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3465 helix: -0.12 (0.15), residues: 1170 sheet: -1.41 (0.22), residues: 493 loop : -1.58 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 166 TYR 0.022 0.002 TYR A1169 PHE 0.036 0.002 PHE B 283 TRP 0.025 0.002 TRP A1050 HIS 0.006 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (29256) covalent geometry : angle 0.62330 / 0.33 (39951) hydrogen bonds : bond 0.03889 / 2.51 ( 1011) hydrogen bonds : angle 5.06581 / 3.53 ( 2868) metal coordination : bond 0.01354 / 0.85 ( 16) metal coordination : angle 5.73548 / 3.85 ( 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 194 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.194 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: 0.8825 (p0) cc_final: 0.8583 (t70) REVERT: A 405 MET cc_start: 0.9080 (pmm) cc_final: 0.8811 (pmm) REVERT: A 406 ASP cc_start: 0.9321 (m-30) cc_final: 0.9099 (m-30) REVERT: A 470 MET cc_start: 0.8311 (mtp) cc_final: 0.8020 (mpp) REVERT: A 491 MET cc_start: 0.7564 (mmm) cc_final: 0.7091 (mmt) REVERT: A 609 MET cc_start: 0.8551 (tpp) cc_final: 0.8345 (tpp) REVERT: A 724 PHE cc_start: 0.9255 (m-80) cc_final: 0.8966 (m-10) REVERT: A 754 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 557 MET cc_start: 0.7819 (ppp) cc_final: 0.7098 (ppp) REVERT: B 786 ASP cc_start: 0.7852 (t70) cc_final: 0.7493 (t0) REVERT: B 1026 MET cc_start: 0.8759 (mmp) cc_final: 0.8386 (mmt) REVERT: C 251 MET cc_start: 0.8181 (mtt) cc_final: 0.7586 (mtt) REVERT: D 150 LYS cc_start: 0.9023 (pttp) cc_final: 0.8763 (mmmt) REVERT: D 152 TYR cc_start: 0.5898 (m-10) cc_final: 0.5536 (t80) REVERT: D 159 MET cc_start: -0.6672 (tpt) cc_final: -0.6958 (tpt) REVERT: E 38 MET cc_start: 0.4229 (tpt) cc_final: 0.3907 (tpt) REVERT: F 65 MET cc_start: 0.7100 (ttt) cc_final: 0.4963 (tmm) REVERT: G 24 MET cc_start: 0.6383 (tmm) cc_final: 0.6161 (tmm) REVERT: G 178 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6734 (pm20) REVERT: K 48 MET cc_start: 0.8365 (mmm) cc_final: 0.7864 (mmm) REVERT: W 627 ARG cc_start: 0.8155 (mtt180) cc_final: 0.6982 (mmm160) REVERT: W 647 PHE cc_start: 0.7371 (t80) cc_final: 0.7074 (t80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1948 time to fit residues: 61.1520 Evaluate side-chains 156 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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: 30.0000 chunk 217 optimal weight: 7.9990 chunk 151 optimal weight: 0.4980 chunk 208 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 302 optimal weight: 40.0000 chunk 312 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 413 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 GLN B 124 GLN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 229 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 653 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.065138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051778 restraints weight = 403410.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.052549 restraints weight = 286001.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.053119 restraints weight = 224365.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.053460 restraints weight = 187795.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.053804 restraints weight = 165419.792| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 29272 Z= 0.183 Angle : 0.656 10.027 39975 Z= 0.340 Chirality : 0.043 0.248 4636 Planarity : 0.005 0.082 4805 Dihedral : 15.792 174.084 4685 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3465 helix: -0.08 (0.15), residues: 1164 sheet: -1.38 (0.22), residues: 503 loop : -1.49 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 714 TYR 0.020 0.002 TYR A1169 PHE 0.022 0.002 PHE A 724 TRP 0.024 0.002 TRP A1050 HIS 0.007 0.001 HIS B 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (29256) covalent geometry : angle 0.64410 / 0.34 (39951) hydrogen bonds : bond 0.04414 / 2.86 ( 1011) hydrogen bonds : angle 5.07838 / 3.54 ( 2868) metal coordination : bond 0.01560 / 1.14 ( 16) metal coordination : angle 5.04516 / 3.53 ( 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 179 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8760 (p0) cc_final: 0.8470 (t0) REVERT: A 405 MET cc_start: 0.9129 (pmm) cc_final: 0.8756 (pmm) REVERT: A 406 ASP cc_start: 0.9294 (m-30) cc_final: 0.9073 (m-30) REVERT: A 470 MET cc_start: 0.8360 (mtp) cc_final: 0.8109 (mpp) REVERT: A 491 MET cc_start: 0.7811 (mmm) cc_final: 0.7262 (mmt) REVERT: A 609 MET cc_start: 0.8577 (tpp) cc_final: 0.8361 (tpp) REVERT: A 724 PHE cc_start: 0.9287 (m-80) cc_final: 0.9002 (m-10) REVERT: A 754 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8800 (mm-30) REVERT: B 557 MET cc_start: 0.7858 (ppp) cc_final: 0.7300 (ppp) REVERT: B 786 ASP cc_start: 0.7944 (t70) cc_final: 0.7613 (t0) REVERT: B 1026 MET cc_start: 0.8816 (mmp) cc_final: 0.8537 (mmm) REVERT: C 251 MET cc_start: 0.8217 (mtt) cc_final: 0.7648 (mtt) REVERT: D 93 MET cc_start: 0.4154 (mmp) cc_final: 0.3274 (mtt) REVERT: D 150 LYS cc_start: 0.9095 (pttp) cc_final: 0.8788 (mmmt) REVERT: D 152 TYR cc_start: 0.5765 (m-10) cc_final: 0.5402 (t80) REVERT: D 159 MET cc_start: -0.6599 (tpt) cc_final: -0.6864 (tpt) REVERT: E 38 MET cc_start: 0.4657 (tpt) cc_final: 0.4032 (tpt) REVERT: G 18 MET cc_start: 0.3016 (mtt) cc_final: 0.2756 (mtp) REVERT: G 178 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7113 (pm20) REVERT: H 121 MET cc_start: 0.8977 (ttm) cc_final: 0.8348 (ttm) REVERT: K 48 MET cc_start: 0.8417 (mmm) cc_final: 0.7905 (mmm) REVERT: W 627 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7048 (mmm160) REVERT: W 647 PHE cc_start: 0.7168 (t80) cc_final: 0.6791 (t80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1860 time to fit residues: 55.0765 Evaluate side-chains 146 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 7.9990 chunk 338 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 249 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 303 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 439 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 852 ASN ** B 947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 229 GLN H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.064242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.050943 restraints weight = 409560.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051729 restraints weight = 289300.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.052294 restraints weight = 225615.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.052697 restraints weight = 188477.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.052913 restraints weight = 164858.062| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29272 Z= 0.177 Angle : 0.650 14.945 39975 Z= 0.336 Chirality : 0.043 0.270 4636 Planarity : 0.005 0.090 4805 Dihedral : 15.859 172.956 4685 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.04 % Allowed : 0.96 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3465 helix: -0.11 (0.15), residues: 1171 sheet: -1.44 (0.23), residues: 479 loop : -1.56 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 605 TYR 0.020 0.002 TYR A1169 PHE 0.021 0.002 PHE A 351 TRP 0.024 0.002 TRP A1050 HIS 0.008 0.001 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (29256) covalent geometry : angle 0.63997 / 0.34 (39951) hydrogen bonds : bond 0.04002 / 2.60 ( 1011) hydrogen bonds : angle 5.08887 / 3.55 ( 2868) metal coordination : bond 0.01762 / 1.14 ( 16) metal coordination : angle 4.63572 / 3.52 ( 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 178 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.014 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: A 133 ASP cc_start: 0.8744 (p0) cc_final: 0.8466 (t0) REVERT: A 405 MET cc_start: 0.9124 (pmm) cc_final: 0.8758 (pmm) REVERT: A 406 ASP cc_start: 0.9212 (m-30) cc_final: 0.8935 (m-30) REVERT: A 470 MET cc_start: 0.8373 (mtp) cc_final: 0.8126 (mpp) REVERT: A 491 MET cc_start: 0.8016 (mmm) cc_final: 0.7495 (mmt) REVERT: A 631 MET cc_start: 0.9206 (tpt) cc_final: 0.8881 (tpp) REVERT: A 724 PHE cc_start: 0.9327 (m-80) cc_final: 0.9005 (m-10) REVERT: A 754 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8772 (mm-30) REVERT: B 557 MET cc_start: 0.7933 (ppp) cc_final: 0.7311 (ppp) REVERT: B 786 ASP cc_start: 0.7901 (t70) cc_final: 0.7491 (t0) REVERT: B 1026 MET cc_start: 0.8822 (mmp) cc_final: 0.8594 (mmm) REVERT: C 251 MET cc_start: 0.8183 (mtt) cc_final: 0.7624 (mtt) REVERT: D 93 MET cc_start: 0.4167 (mmp) cc_final: 0.2754 (mtt) REVERT: D 150 LYS cc_start: 0.9095 (pttp) cc_final: 0.8802 (mmmt) REVERT: D 152 TYR cc_start: 0.5867 (m-10) cc_final: 0.5543 (t80) REVERT: D 159 MET cc_start: -0.6547 (tpt) cc_final: -0.6771 (tpt) REVERT: E 38 MET cc_start: 0.5022 (tpt) cc_final: 0.4445 (tpt) REVERT: F 65 MET cc_start: 0.7407 (ttt) cc_final: 0.6768 (tmm) REVERT: G 178 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7157 (pm20) REVERT: H 121 MET cc_start: 0.8888 (ttm) cc_final: 0.8328 (ttp) REVERT: K 48 MET cc_start: 0.8473 (mmm) cc_final: 0.7947 (mmm) REVERT: W 627 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7115 (mmm160) REVERT: W 647 PHE cc_start: 0.7007 (t80) cc_final: 0.6622 (t80) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1780 time to fit residues: 52.3493 Evaluate side-chains 143 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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: 9.9990 chunk 170 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 957 HIS A1100 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.063322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.050209 restraints weight = 412073.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.050960 restraints weight = 290932.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.051525 restraints weight = 227383.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.051847 restraints weight = 189407.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.052184 restraints weight = 167112.119| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 29272 Z= 0.186 Angle : 0.667 11.404 39975 Z= 0.345 Chirality : 0.043 0.254 4636 Planarity : 0.005 0.049 4805 Dihedral : 15.927 171.860 4685 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.22 % 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 are not related in a simple way. whole: -1.59 (0.14), residues: 3465 helix: -0.10 (0.15), residues: 1173 sheet: -1.52 (0.23), residues: 487 loop : -1.55 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 184 TYR 0.021 0.002 TYR B1037 PHE 0.022 0.002 PHE B 746 TRP 0.027 0.002 TRP B 229 HIS 0.008 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (29256) covalent geometry : angle 0.65413 / 0.34 (39951) hydrogen bonds : bond 0.04351 / 2.80 ( 1011) hydrogen bonds : angle 5.14379 / 3.57 ( 2868) metal coordination : bond 0.01386 / 0.98 ( 16) metal coordination : angle 5.27836 / 3.63 ( 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 170 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.763 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: A 133 ASP cc_start: 0.8673 (p0) cc_final: 0.8396 (t0) REVERT: A 405 MET cc_start: 0.9146 (pmm) cc_final: 0.8752 (pmm) REVERT: A 491 MET cc_start: 0.8103 (mmm) cc_final: 0.7662 (mmt) REVERT: A 609 MET cc_start: 0.8681 (tpp) cc_final: 0.8424 (tpp) REVERT: A 631 MET cc_start: 0.9222 (tpt) cc_final: 0.8935 (tpp) REVERT: A 724 PHE cc_start: 0.9329 (m-80) cc_final: 0.9051 (m-10) REVERT: B 422 MET cc_start: 0.8153 (mtt) cc_final: 0.7952 (mtt) REVERT: B 557 MET cc_start: 0.8071 (ppp) cc_final: 0.7533 (ppp) REVERT: B 786 ASP cc_start: 0.8039 (t70) cc_final: 0.7656 (t0) REVERT: B 854 MET cc_start: 0.9521 (mmm) cc_final: 0.9310 (mmm) REVERT: B 1026 MET cc_start: 0.8794 (mmp) cc_final: 0.8584 (mmm) REVERT: C 251 MET cc_start: 0.8278 (mtt) cc_final: 0.7681 (mtt) REVERT: D 93 MET cc_start: 0.4326 (mmp) cc_final: 0.1514 (mtt) REVERT: F 65 MET cc_start: 0.7469 (ttt) cc_final: 0.5474 (tmm) REVERT: G 18 MET cc_start: 0.3093 (mtt) cc_final: 0.2874 (mtp) REVERT: G 178 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7373 (pm20) REVERT: H 121 MET cc_start: 0.8942 (ttm) cc_final: 0.8735 (ttm) REVERT: K 48 MET cc_start: 0.8543 (mmm) cc_final: 0.8032 (mmm) REVERT: W 627 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7105 (mmm160) REVERT: W 647 PHE cc_start: 0.7067 (t80) cc_final: 0.6632 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1728 time to fit residues: 48.5557 Evaluate side-chains 137 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 273 optimal weight: 0.6980 chunk 227 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.063931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.050685 restraints weight = 404228.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.051475 restraints weight = 286165.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.052044 restraints weight = 223035.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.052428 restraints weight = 186056.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.052666 restraints weight = 163323.499| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29272 Z= 0.126 Angle : 0.617 10.285 39975 Z= 0.317 Chirality : 0.042 0.278 4636 Planarity : 0.004 0.050 4805 Dihedral : 15.874 170.638 4685 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % 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 are not related in a simple way. whole: -1.45 (0.14), residues: 3465 helix: 0.04 (0.15), residues: 1178 sheet: -1.46 (0.23), residues: 470 loop : -1.49 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 530 TYR 0.019 0.001 TYR A 163 PHE 0.031 0.001 PHE D 98 TRP 0.019 0.001 TRP A1050 HIS 0.009 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (29256) covalent geometry : angle 0.60681 / 0.32 (39951) hydrogen bonds : bond 0.03650 / 2.31 ( 1011) hydrogen bonds : angle 4.96329 / 3.45 ( 2868) metal coordination : bond 0.00840 / 0.61 ( 16) metal coordination : angle 4.52831 / 3.21 ( 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 174 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.8715 (p0) cc_final: 0.8433 (t0) REVERT: A 405 MET cc_start: 0.9188 (pmm) cc_final: 0.8793 (pmm) REVERT: A 406 ASP cc_start: 0.9207 (m-30) cc_final: 0.8938 (m-30) REVERT: A 470 MET cc_start: 0.8649 (mtm) cc_final: 0.8189 (mpp) REVERT: A 491 MET cc_start: 0.8134 (mmm) cc_final: 0.7746 (mmt) REVERT: A 609 MET cc_start: 0.8630 (tpp) cc_final: 0.8347 (tpp) REVERT: A 631 MET cc_start: 0.9220 (tpt) cc_final: 0.8979 (tpp) REVERT: A 724 PHE cc_start: 0.9320 (m-80) cc_final: 0.9087 (m-10) REVERT: A 754 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8912 (mm-30) REVERT: A 971 LYS cc_start: 0.8121 (mppt) cc_final: 0.7915 (mmmt) REVERT: B 557 MET cc_start: 0.8019 (ppp) cc_final: 0.7418 (ppp) REVERT: B 786 ASP cc_start: 0.7980 (t70) cc_final: 0.7575 (t0) REVERT: C 251 MET cc_start: 0.8216 (mtt) cc_final: 0.7645 (mtt) REVERT: D 93 MET cc_start: 0.4380 (mmp) cc_final: 0.1332 (mtt) REVERT: D 150 LYS cc_start: 0.9088 (pttp) cc_final: 0.8883 (ptpp) REVERT: E 38 MET cc_start: 0.5554 (tpt) cc_final: 0.5257 (tpt) REVERT: F 65 MET cc_start: 0.7369 (ttt) cc_final: 0.6888 (tmm) REVERT: G 18 MET cc_start: 0.3108 (mtt) cc_final: 0.2886 (mtp) REVERT: G 24 MET cc_start: 0.6609 (tmm) cc_final: 0.6065 (tmm) REVERT: G 178 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7371 (pm20) REVERT: H 41 MET cc_start: 0.9059 (tmm) cc_final: 0.8808 (tmm) REVERT: H 121 MET cc_start: 0.8881 (ttm) cc_final: 0.8086 (ttp) REVERT: K 48 MET cc_start: 0.8493 (mmm) cc_final: 0.8019 (mmm) REVERT: W 627 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7140 (mmm160) REVERT: W 647 PHE cc_start: 0.7138 (t80) cc_final: 0.6804 (t80) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1659 time to fit residues: 47.8661 Evaluate side-chains 139 residues out of total 3130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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: 0.2980 chunk 195 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN ** B 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS H 137 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.064725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.051272 restraints weight = 397599.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.052085 restraints weight = 280548.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.052657 restraints weight = 219054.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.053044 restraints weight = 182829.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.053299 restraints weight = 160051.104| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29272 Z= 0.111 Angle : 0.600 16.282 39975 Z= 0.306 Chirality : 0.042 0.271 4636 Planarity : 0.004 0.051 4805 Dihedral : 15.812 170.624 4685 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % 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 are not related in a simple way. whole: -1.26 (0.14), residues: 3465 helix: 0.23 (0.15), residues: 1169 sheet: -1.36 (0.23), residues: 489 loop : -1.39 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 494 TYR 0.027 0.001 TYR B 442 PHE 0.024 0.001 PHE H 24 TRP 0.016 0.001 TRP B 229 HIS 0.005 0.001 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (29256) covalent geometry : angle 0.59010 / 0.31 (39951) hydrogen bonds : bond 0.03386 / 2.16 ( 1011) hydrogen bonds : angle 4.81824 / 3.35 ( 2868) metal coordination : bond 0.00680 / 0.48 ( 16) metal coordination : angle 4.40996 / 3.07 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5673.70 seconds wall clock time: 98 minutes 48.32 seconds (5928.32 seconds total)