Starting phenix.real_space_refine on Fri Aug 7 01:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1r_61980/08_2026/9k1r_61980.cif" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 40 5.49 5 S 102 5.16 5 C 11226 2.51 5 N 3068 2.21 5 O 3439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17878 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 6478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6478 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 34, 'TRANS': 779} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9158 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 60, 'TRANS': 1107} Chain breaks: 5 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 584 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 528 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 21} Chain: "H" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 316 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6647 SG CYS D 23 85.022 65.157 40.628 1.00 17.70 S ATOM 6671 SG CYS D 26 82.539 62.558 41.633 1.00 17.93 S ATOM 6918 SG CYS D 58 84.453 64.557 44.346 1.00 17.77 S ATOM 6939 SG CYS D 61 86.324 62.032 42.295 1.00 14.34 S ATOM 6560 SG CYS D 11 86.884 60.074 59.571 1.00 18.56 S ATOM 6823 SG CYS D 46 86.657 63.951 60.207 1.00 24.02 S ATOM 6846 SG CYS D 49 87.958 62.690 57.031 1.00 26.62 S ATOM 7117 SG CYS D 85 84.215 62.153 57.949 1.00 19.29 S ATOM 6698 SG CYS D 30 72.270 61.888 48.425 1.00 14.07 S ATOM 6719 SG CYS D 33 70.571 58.591 47.690 1.00 15.66 S ATOM 7014 SG CYS D 72 68.443 61.529 48.585 1.00 15.87 S ATOM 7038 SG CYS D 75 70.522 59.970 51.284 1.00 20.17 S Time building chain proxies: 3.87, per 1000 atoms: 0.22 Number of scatterers: 17878 At special positions: 0 Unit cell: (137.5, 144.1, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 102 16.00 P 40 15.00 O 3439 8.00 N 3068 7.00 C 11226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 773.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 26 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " Number of angles added : 18 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 26 sheets defined 40.4% alpha, 18.0% beta 14 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'C' and resid 508 through 523 removed outlier: 3.528A pdb=" N ARG C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 541 Proline residue: C 537 - end of helix removed outlier: 3.558A pdb=" N SER C 541 " --> pdb=" O PRO C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 561 removed outlier: 4.287A pdb=" N TYR C 561 " --> pdb=" O ASP C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 584 removed outlier: 3.833A pdb=" N VAL C 577 " --> pdb=" O LYS C 573 " (cutoff:3.500A) Proline residue: C 580 - end of helix removed outlier: 3.793A pdb=" N ASP C 584 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 621 through 638 Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 657 through 676 removed outlier: 3.914A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 676 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'C' and resid 683 through 692 removed outlier: 4.121A pdb=" N ILE C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 698 through 716 removed outlier: 3.692A pdb=" N ARG C 702 " --> pdb=" O GLN C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 727 through 736 removed outlier: 3.562A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.617A pdb=" N ALA C 762 " --> pdb=" O ASP C 758 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN C 778 " --> pdb=" O ILE C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 797 Processing helix chain 'C' and resid 802 through 818 removed outlier: 3.992A pdb=" N LEU C 811 " --> pdb=" O LYS C 807 " (cutoff:3.500A) Proline residue: C 812 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.259A pdb=" N ASP C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 845 removed outlier: 3.704A pdb=" N TYR C 830 " --> pdb=" O ASP C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 855 removed outlier: 4.177A pdb=" N ASP C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 859 Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 885 through 902 removed outlier: 3.764A pdb=" N GLU C 902 " --> pdb=" O TYR C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 922 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'C' and resid 942 through 946 removed outlier: 3.643A pdb=" N ALA C 945 " --> pdb=" O ASN C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 965 removed outlier: 4.902A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 981 Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 986 through 1004 Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1051 through 1066 removed outlier: 3.690A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1088 Processing helix chain 'C' and resid 1091 through 1099 Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.683A pdb=" N ARG C1109 " --> pdb=" O GLU C1105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C1110 " --> pdb=" O ARG C1106 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1134 removed outlier: 3.851A pdb=" N ASN C1134 " --> pdb=" O PRO C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 3.625A pdb=" N GLN C1144 " --> pdb=" O GLU C1140 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C1159 " --> pdb=" O PHE C1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1167 removed outlier: 3.793A pdb=" N ILE C1166 " --> pdb=" O LYS C1163 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR C1167 " --> pdb=" O ASP C1164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1163 through 1167' Processing helix chain 'C' and resid 1169 through 1177 Processing helix chain 'C' and resid 1181 through 1199 Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 4.201A pdb=" N HIS C1210 " --> pdb=" O ASP C1206 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C1211 " --> pdb=" O SER C1207 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C1212 " --> pdb=" O LEU C1208 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C1213 " --> pdb=" O ASN C1209 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1220 removed outlier: 4.307A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1220' Processing helix chain 'C' and resid 1223 through 1242 removed outlier: 3.834A pdb=" N VAL C1239 " --> pdb=" O GLU C1235 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C1240 " --> pdb=" O GLY C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1254 removed outlier: 4.538A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN C1252 " --> pdb=" O GLN C1248 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C1253 " --> pdb=" O TYR C1249 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1275 removed outlier: 3.971A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1302 removed outlier: 3.579A pdb=" N LEU C1300 " --> pdb=" O ARG C1297 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C1302 " --> pdb=" O GLU C1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.555A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.522A pdb=" N ARG A 432 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 removed outlier: 4.179A pdb=" N GLU A 562 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.857A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 826 Processing helix chain 'A' and resid 837 through 845 removed outlier: 3.919A pdb=" N GLU A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 3.779A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1175 through 1181 removed outlier: 4.099A pdb=" N CYS A1179 " --> pdb=" O ASP A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1198 Processing helix chain 'A' and resid 1200 through 1215 removed outlier: 4.040A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.734A pdb=" N TRP B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 57 removed outlier: 3.750A pdb=" N PHE B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.037A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.148A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 4.009A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A1120 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A1174 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.777A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG A 42 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR A 52 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 69 removed outlier: 7.950A pdb=" N ASP A 76 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR A 92 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS A 103 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU A 91 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS A 101 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN A 93 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 99 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 173 removed outlier: 5.680A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 235 through 238 removed outlier: 4.232A pdb=" N GLY A 247 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 267 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.530A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 294 removed outlier: 7.124A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 292 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 300 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 315 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 303 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 331 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS A 312 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR A 329 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 287 through 294 removed outlier: 7.124A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 292 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 300 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 315 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 303 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 336 through 341 removed outlier: 4.105A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 357 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.732A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 449 through 450 removed outlier: 4.282A pdb=" N PHE A 741 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.590A pdb=" N VAL A 462 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 486 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 492 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 516 through 520 removed outlier: 3.670A pdb=" N TYR A 520 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 546 through 548 removed outlier: 3.746A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 554 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 566 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 587 through 592 removed outlier: 4.368A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 606 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 637 through 643 removed outlier: 4.243A pdb=" N SER A 639 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 668 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS A 641 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 666 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.607A pdb=" N VAL A 704 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 711 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 724 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR A 723 " --> pdb=" O HIS A 730 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS A 730 " --> pdb=" O TYR A 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.172A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 868 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.731A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 890 " --> pdb=" O GLY A 908 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 892 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 906 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 949 through 955 removed outlier: 5.146A pdb=" N ALA A 951 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY A 962 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 953 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 959 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS A 981 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP A 971 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG A 979 " --> pdb=" O ASP A 971 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 990 through 995 removed outlier: 3.739A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A1024 " --> pdb=" O TRP A1011 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1038 through 1040 removed outlier: 6.668A pdb=" N THR A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A1090 " --> pdb=" O ARG A1057 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4728 1.33 - 1.45: 3336 1.45 - 1.58: 10012 1.58 - 1.70: 78 1.70 - 1.82: 157 Bond restraints: 18311 Sorted by residual: bond pdb=" N7 G H 12 " pdb=" C5 G H 12 " ideal model delta sigma weight residual 1.388 1.377 0.011 6.00e-03 2.78e+04 3.50e+00 bond pdb=" C THR C 717 " pdb=" N PRO C 718 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.30e-02 5.92e+03 1.88e+00 bond pdb=" C8 G H 12 " pdb=" N7 G H 12 " ideal model delta sigma weight residual 1.305 1.297 0.008 6.00e-03 2.78e+04 1.67e+00 bond pdb=" N1 U H 11 " pdb=" C2 U H 11 " ideal model delta sigma weight residual 1.381 1.392 -0.011 9.00e-03 1.23e+04 1.53e+00 bond pdb=" CG GLU C 595 " pdb=" CD GLU C 595 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 18306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 24533 1.76 - 3.52: 384 3.52 - 5.28: 48 5.28 - 7.04: 20 7.04 - 8.81: 5 Bond angle restraints: 24990 Sorted by residual: angle pdb=" N VAL C 727 " pdb=" CA VAL C 727 " pdb=" C VAL C 727 " ideal model delta sigma weight residual 113.47 107.99 5.48 1.01e+00 9.80e-01 2.95e+01 angle pdb=" O2 U H 11 " pdb=" C2 U H 11 " pdb=" N3 U H 11 " ideal model delta sigma weight residual 122.20 119.05 3.15 7.00e-01 2.04e+00 2.02e+01 angle pdb=" C1' U H 11 " pdb=" N1 U H 11 " pdb=" C2 U H 11 " ideal model delta sigma weight residual 117.70 123.03 -5.33 1.20e+00 6.94e-01 1.97e+01 angle pdb=" C1' C H 10 " pdb=" N1 C H 10 " pdb=" C2 C H 10 " ideal model delta sigma weight residual 118.80 123.39 -4.59 1.10e+00 8.26e-01 1.74e+01 angle pdb=" O5' U H 4 " pdb=" C5' U H 4 " pdb=" C4' U H 4 " ideal model delta sigma weight residual 109.40 112.71 -3.31 8.00e-01 1.56e+00 1.71e+01 ... (remaining 24985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 10730 31.12 - 62.24: 373 62.24 - 93.36: 47 93.36 - 124.48: 0 124.48 - 155.60: 1 Dihedral angle restraints: 11151 sinusoidal: 4879 harmonic: 6272 Sorted by residual: dihedral pdb=" O4' U G 46 " pdb=" C1' U G 46 " pdb=" N1 U G 46 " pdb=" C2 U G 46 " ideal model delta sinusoidal sigma weight residual 200.00 44.40 155.60 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" CA GLU B 70 " pdb=" C GLU B 70 " pdb=" N LYS B 71 " pdb=" CA LYS B 71 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU A 136 " pdb=" C GLU A 136 " pdb=" N LYS A 137 " pdb=" CA LYS A 137 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2042 0.036 - 0.072: 516 0.072 - 0.108: 220 0.108 - 0.144: 89 0.144 - 0.180: 3 Chirality restraints: 2870 Sorted by residual: chirality pdb=" CA ARG C 614 " pdb=" N ARG C 614 " pdb=" C ARG C 614 " pdb=" CB ARG C 614 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA THR C1010 " pdb=" N THR C1010 " pdb=" C THR C1010 " pdb=" CB THR C1010 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA THR C1170 " pdb=" N THR C1170 " pdb=" C THR C1170 " pdb=" CB THR C1170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 2867 not shown) Planarity restraints: 3076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 647 " -0.001 2.00e-02 2.50e+03 1.46e-02 3.72e+00 pdb=" CG PHE C 647 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 647 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 647 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE C 647 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 647 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 647 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 509 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO C 510 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 508 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C 509 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " 0.021 5.00e-02 4.00e+02 ... (remaining 3073 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 734 2.72 - 3.27: 17009 3.27 - 3.81: 28328 3.81 - 4.36: 32003 4.36 - 4.90: 56192 Nonbonded interactions: 134266 Sorted by model distance: nonbonded pdb=" OG1 THR A 165 " pdb=" OE2 GLU A 186 " model vdw 2.179 3.040 nonbonded pdb=" OE1 GLU C 890 " pdb=" OH TYR C 928 " model vdw 2.208 3.040 nonbonded pdb=" O THR A 52 " pdb=" OH TYR A 725 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 317 " pdb=" O MET A 321 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN C1107 " pdb=" N4 C G 37 " model vdw 2.284 3.120 ... (remaining 134261 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.002 0.030 18323 Z= 0.104 Angle : 0.534 8.806 25008 Z= 0.312 Chirality : 0.043 0.180 2870 Planarity : 0.003 0.039 3076 Dihedral : 15.141 155.603 7111 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2140 helix: 1.90 (0.20), residues: 739 sheet: 0.35 (0.27), residues: 431 loop : -1.63 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 614 TYR 0.022 0.001 TYR C 898 PHE 0.026 0.001 PHE C 647 TRP 0.018 0.001 TRP C1055 HIS 0.011 0.000 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (18311) covalent geometry : angle 0.52888 / 0.31 (24990) hydrogen bonds : bond 0.18032 / 12.31 ( 757) hydrogen bonds : angle 7.15617 / 5.20 ( 2116) metal coordination : bond 0.00249 / 0.15 ( 12) metal coordination : angle 2.87867 / 1.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: C 540 MET cc_start: 0.3942 (ppp) cc_final: 0.2899 (tpt) REVERT: C 776 GLU cc_start: 0.6374 (mp0) cc_final: 0.6091 (mp0) REVERT: D 9 ILE cc_start: 0.8494 (mt) cc_final: 0.8203 (mt) REVERT: D 105 TYR cc_start: 0.5427 (m-80) cc_final: 0.5063 (m-80) REVERT: A 1 MET cc_start: 0.7002 (ptp) cc_final: 0.6640 (ptp) REVERT: A 590 MET cc_start: 0.3230 (tpt) cc_final: 0.2360 (mpp) REVERT: A 706 MET cc_start: 0.1812 (tpt) cc_final: 0.1436 (tpt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1245 time to fit residues: 54.8638 Evaluate side-chains 211 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 533 ASN D 50 ASN A 666 ASN A 870 ASN A1087 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.166007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130891 restraints weight = 34775.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.128672 restraints weight = 34501.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130239 restraints weight = 31011.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130295 restraints weight = 22696.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130395 restraints weight = 21328.314| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18323 Z= 0.233 Angle : 0.684 11.775 25008 Z= 0.349 Chirality : 0.046 0.166 2870 Planarity : 0.005 0.046 3076 Dihedral : 11.547 154.407 2960 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.50 % Allowed : 10.08 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2140 helix: 1.44 (0.19), residues: 751 sheet: -0.18 (0.25), residues: 428 loop : -1.77 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 495 TYR 0.025 0.002 TYR C1273 PHE 0.024 0.002 PHE C 647 TRP 0.010 0.002 TRP B 29 HIS 0.008 0.002 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (18311) covalent geometry : angle 0.66725 / 0.35 (24990) hydrogen bonds : bond 0.05132 / 3.46 ( 757) hydrogen bonds : angle 5.61477 / 4.13 ( 2116) metal coordination : bond 0.01030 / 0.66 ( 12) metal coordination : angle 5.71914 / 3.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: C 540 MET cc_start: 0.4016 (ppp) cc_final: 0.3057 (tpt) REVERT: C 623 TYR cc_start: 0.7166 (t80) cc_final: 0.6386 (t80) REVERT: C 1056 MET cc_start: 0.7785 (tpp) cc_final: 0.7562 (mmm) REVERT: C 1246 MET cc_start: 0.7895 (mpp) cc_final: 0.7657 (mpp) REVERT: A 583 MET cc_start: 0.0345 (mpp) cc_final: -0.0927 (tmm) REVERT: A 706 MET cc_start: 0.2302 (tpt) cc_final: 0.1970 (tpt) outliers start: 28 outliers final: 22 residues processed: 233 average time/residue: 0.1228 time to fit residues: 44.9633 Evaluate side-chains 211 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1055 TRP Chi-restraints excluded: chain C residue 1099 ASN Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1150 SER Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 124 optimal weight: 0.0980 chunk 6 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.165641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131319 restraints weight = 35061.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129127 restraints weight = 36663.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130376 restraints weight = 31182.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130674 restraints weight = 22227.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130914 restraints weight = 20616.799| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18323 Z= 0.157 Angle : 0.592 10.364 25008 Z= 0.298 Chirality : 0.043 0.219 2870 Planarity : 0.004 0.048 3076 Dihedral : 11.541 153.951 2960 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.93 % Allowed : 12.33 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2140 helix: 1.54 (0.20), residues: 751 sheet: -0.30 (0.25), residues: 444 loop : -1.77 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 495 TYR 0.036 0.001 TYR C1083 PHE 0.014 0.001 PHE C 647 TRP 0.009 0.001 TRP C1216 HIS 0.007 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (18311) covalent geometry : angle 0.57479 / 0.30 (24990) hydrogen bonds : bond 0.04597 / 3.11 ( 757) hydrogen bonds : angle 5.27727 / 3.87 ( 2116) metal coordination : bond 0.00702 / 0.41 ( 12) metal coordination : angle 5.37075 / 3.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 495 ARG cc_start: 0.7606 (mmp80) cc_final: 0.7404 (mmp80) REVERT: C 540 MET cc_start: 0.4188 (ppp) cc_final: 0.3025 (tpt) REVERT: C 623 TYR cc_start: 0.7096 (t80) cc_final: 0.6420 (t80) REVERT: D 50 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 583 MET cc_start: 0.0503 (mpp) cc_final: -0.0738 (tmm) REVERT: A 706 MET cc_start: 0.2446 (tpt) cc_final: 0.2125 (tpt) outliers start: 36 outliers final: 26 residues processed: 229 average time/residue: 0.1244 time to fit residues: 44.8000 Evaluate side-chains 211 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 199 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130602 restraints weight = 34928.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128375 restraints weight = 32950.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130148 restraints weight = 30299.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129834 restraints weight = 21012.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130294 restraints weight = 19433.147| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18323 Z= 0.150 Angle : 0.595 10.954 25008 Z= 0.297 Chirality : 0.044 0.372 2870 Planarity : 0.004 0.048 3076 Dihedral : 11.536 153.418 2960 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.20 % Allowed : 14.16 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.18), residues: 2140 helix: 1.49 (0.19), residues: 751 sheet: -0.37 (0.25), residues: 448 loop : -1.83 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.047 0.001 TYR C1083 PHE 0.014 0.001 PHE C 647 TRP 0.009 0.001 TRP C1055 HIS 0.004 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18311) covalent geometry : angle 0.57724 / 0.30 (24990) hydrogen bonds : bond 0.04363 / 2.93 ( 757) hydrogen bonds : angle 5.12565 / 3.74 ( 2116) metal coordination : bond 0.00712 / 0.40 ( 12) metal coordination : angle 5.41203 / 3.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 495 ARG cc_start: 0.7525 (mmp80) cc_final: 0.7226 (mmp80) REVERT: C 623 TYR cc_start: 0.7178 (t80) cc_final: 0.6445 (t80) REVERT: A 583 MET cc_start: 0.0288 (mpp) cc_final: -0.0877 (tmm) REVERT: A 706 MET cc_start: 0.2395 (tpt) cc_final: 0.2054 (tpt) outliers start: 41 outliers final: 29 residues processed: 227 average time/residue: 0.1271 time to fit residues: 45.6723 Evaluate side-chains 213 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 175 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126832 restraints weight = 35151.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123368 restraints weight = 37394.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124824 restraints weight = 34804.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125148 restraints weight = 24042.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125242 restraints weight = 22268.186| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18323 Z= 0.243 Angle : 0.706 14.753 25008 Z= 0.359 Chirality : 0.047 0.265 2870 Planarity : 0.005 0.052 3076 Dihedral : 11.795 150.586 2960 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.11 % Allowed : 15.71 % Favored : 81.18 % 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: -1.02 (0.18), residues: 2140 helix: 0.96 (0.19), residues: 753 sheet: -0.73 (0.24), residues: 442 loop : -2.04 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1013 TYR 0.067 0.002 TYR C1083 PHE 0.018 0.002 PHE A 774 TRP 0.010 0.002 TRP B 29 HIS 0.008 0.002 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (18311) covalent geometry : angle 0.68240 / 0.36 (24990) hydrogen bonds : bond 0.05732 / 3.85 ( 757) hydrogen bonds : angle 5.40463 / 3.92 ( 2116) metal coordination : bond 0.01016 / 0.63 ( 12) metal coordination : angle 6.85040 / 4.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 495 ARG cc_start: 0.7553 (mmp80) cc_final: 0.7278 (mmp80) REVERT: C 623 TYR cc_start: 0.7120 (t80) cc_final: 0.6429 (t80) REVERT: C 1161 MET cc_start: 0.8330 (mmt) cc_final: 0.8093 (mmm) REVERT: C 1254 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 187 MET cc_start: 0.7543 (tpp) cc_final: 0.7285 (tpp) REVERT: A 230 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: A 706 MET cc_start: 0.2623 (tpt) cc_final: 0.2239 (tpt) outliers start: 58 outliers final: 41 residues processed: 233 average time/residue: 0.1304 time to fit residues: 48.1683 Evaluate side-chains 220 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 910 MET Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1055 TRP Chi-restraints excluded: chain C residue 1060 PHE Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1099 ASN Chi-restraints excluded: chain C residue 1121 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1272 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1210 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 101 optimal weight: 1.9990 chunk 138 optimal weight: 0.0030 chunk 179 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129313 restraints weight = 34593.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127957 restraints weight = 34253.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128760 restraints weight = 29972.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129033 restraints weight = 21049.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129161 restraints weight = 19649.259| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18323 Z= 0.124 Angle : 0.599 11.467 25008 Z= 0.299 Chirality : 0.043 0.247 2870 Planarity : 0.004 0.049 3076 Dihedral : 11.708 151.254 2960 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.04 % Allowed : 17.59 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2140 helix: 1.21 (0.19), residues: 753 sheet: -0.56 (0.25), residues: 433 loop : -1.93 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 21 TYR 0.052 0.001 TYR C1083 PHE 0.013 0.001 PHE C 647 TRP 0.009 0.001 TRP C1216 HIS 0.009 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (18311) covalent geometry : angle 0.57950 / 0.30 (24990) hydrogen bonds : bond 0.04264 / 2.84 ( 757) hydrogen bonds : angle 5.03845 / 3.67 ( 2116) metal coordination : bond 0.00545 / 0.33 ( 12) metal coordination : angle 5.60802 / 3.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 495 ARG cc_start: 0.7536 (mmp80) cc_final: 0.7309 (mmp80) REVERT: C 623 TYR cc_start: 0.7025 (t80) cc_final: 0.6361 (t80) REVERT: C 675 MET cc_start: 0.7360 (mmp) cc_final: 0.7128 (mmm) REVERT: C 954 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8285 (mm) REVERT: C 1056 MET cc_start: 0.7605 (tpp) cc_final: 0.7359 (tpp) REVERT: C 1161 MET cc_start: 0.8191 (mmt) cc_final: 0.7929 (mmm) REVERT: A 706 MET cc_start: 0.2674 (tpt) cc_final: 0.2201 (tpt) outliers start: 38 outliers final: 31 residues processed: 225 average time/residue: 0.1286 time to fit residues: 45.8381 Evaluate side-chains 213 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 954 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1023 ILE Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1055 TRP Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 182 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 chunk 210 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN A1147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130242 restraints weight = 34752.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128754 restraints weight = 31027.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130128 restraints weight = 28963.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129991 restraints weight = 19613.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130445 restraints weight = 18412.410| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18323 Z= 0.108 Angle : 0.600 20.367 25008 Z= 0.292 Chirality : 0.043 0.236 2870 Planarity : 0.004 0.048 3076 Dihedral : 11.623 152.405 2960 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.82 % Allowed : 18.71 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2140 helix: 1.32 (0.19), residues: 752 sheet: -0.44 (0.25), residues: 431 loop : -1.86 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 21 TYR 0.053 0.001 TYR C1083 PHE 0.013 0.001 PHE C 647 TRP 0.008 0.001 TRP C 938 HIS 0.011 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (18311) covalent geometry : angle 0.58317 / 0.29 (24990) hydrogen bonds : bond 0.03772 / 2.53 ( 757) hydrogen bonds : angle 4.85289 / 3.53 ( 2116) metal coordination : bond 0.00481 / 0.32 ( 12) metal coordination : angle 5.29976 / 3.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 623 TYR cc_start: 0.6981 (t80) cc_final: 0.6350 (t80) REVERT: C 699 GLN cc_start: 0.6887 (pm20) cc_final: 0.6603 (pm20) REVERT: C 954 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8291 (mm) REVERT: C 1056 MET cc_start: 0.7539 (tpp) cc_final: 0.7320 (tpp) REVERT: A 706 MET cc_start: 0.2561 (tpt) cc_final: 0.2097 (tpt) outliers start: 34 outliers final: 27 residues processed: 225 average time/residue: 0.1216 time to fit residues: 44.2376 Evaluate side-chains 218 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 954 LEU Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1055 TRP Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 141 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 214 optimal weight: 50.0000 chunk 52 optimal weight: 0.0970 chunk 146 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 0.0050 chunk 37 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.166441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132477 restraints weight = 34740.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130689 restraints weight = 33511.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131806 restraints weight = 30344.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132066 restraints weight = 20931.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.132232 restraints weight = 19424.560| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18323 Z= 0.104 Angle : 0.583 15.995 25008 Z= 0.286 Chirality : 0.042 0.227 2870 Planarity : 0.004 0.048 3076 Dihedral : 11.567 153.668 2960 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.77 % Allowed : 18.93 % Favored : 79.30 % 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: -0.53 (0.18), residues: 2140 helix: 1.35 (0.19), residues: 749 sheet: -0.31 (0.25), residues: 438 loop : -1.80 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 21 TYR 0.048 0.001 TYR C1083 PHE 0.013 0.001 PHE C 647 TRP 0.011 0.001 TRP C1055 HIS 0.011 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (18311) covalent geometry : angle 0.56972 / 0.29 (24990) hydrogen bonds : bond 0.03399 / 2.29 ( 757) hydrogen bonds : angle 4.70425 / 3.42 ( 2116) metal coordination : bond 0.00410 / 0.27 ( 12) metal coordination : angle 4.67270 / 2.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 540 MET cc_start: 0.3585 (ppp) cc_final: 0.2347 (tpp) REVERT: C 623 TYR cc_start: 0.6912 (t80) cc_final: 0.6347 (t80) REVERT: C 1056 MET cc_start: 0.7518 (tpp) cc_final: 0.7311 (tpp) REVERT: A 447 MET cc_start: 0.3182 (mpp) cc_final: 0.2119 (mmm) REVERT: A 706 MET cc_start: 0.2535 (tpt) cc_final: 0.2072 (tpt) outliers start: 33 outliers final: 28 residues processed: 229 average time/residue: 0.1237 time to fit residues: 45.5460 Evaluate side-chains 218 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 200 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS ** C1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129912 restraints weight = 34895.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127514 restraints weight = 34923.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128642 restraints weight = 32452.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128933 restraints weight = 22775.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129117 restraints weight = 21393.535| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18323 Z= 0.153 Angle : 0.621 14.639 25008 Z= 0.305 Chirality : 0.044 0.285 2870 Planarity : 0.004 0.050 3076 Dihedral : 11.573 153.162 2960 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.88 % Allowed : 19.25 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2140 helix: 1.33 (0.19), residues: 753 sheet: -0.43 (0.25), residues: 443 loop : -1.82 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 948 TYR 0.046 0.001 TYR C1083 PHE 0.011 0.001 PHE C 647 TRP 0.024 0.001 TRP C 658 HIS 0.012 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (18311) covalent geometry : angle 0.60551 / 0.30 (24990) hydrogen bonds : bond 0.03931 / 2.65 ( 757) hydrogen bonds : angle 4.80862 / 3.50 ( 2116) metal coordination : bond 0.00629 / 0.41 ( 12) metal coordination : angle 5.24949 / 3.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 623 TYR cc_start: 0.6905 (t80) cc_final: 0.6350 (t80) REVERT: C 655 LYS cc_start: 0.8089 (tptp) cc_final: 0.7885 (tptt) REVERT: A 447 MET cc_start: 0.3122 (mpp) cc_final: 0.1828 (mmm) REVERT: A 706 MET cc_start: 0.2806 (tpt) cc_final: 0.2318 (tpt) outliers start: 35 outliers final: 31 residues processed: 214 average time/residue: 0.1174 time to fit residues: 40.6847 Evaluate side-chains 215 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 30.0000 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 197 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS C1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.163186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128887 restraints weight = 34686.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126759 restraints weight = 35930.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128015 restraints weight = 32992.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128388 restraints weight = 22841.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128468 restraints weight = 21313.860| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18323 Z= 0.141 Angle : 0.629 14.216 25008 Z= 0.308 Chirality : 0.044 0.304 2870 Planarity : 0.004 0.050 3076 Dihedral : 11.610 152.704 2960 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.82 % Allowed : 19.25 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2140 helix: 1.24 (0.19), residues: 754 sheet: -0.49 (0.25), residues: 435 loop : -1.84 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.047 0.001 TYR C1083 PHE 0.019 0.001 PHE C 777 TRP 0.011 0.001 TRP C 658 HIS 0.012 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (18311) covalent geometry : angle 0.61148 / 0.31 (24990) hydrogen bonds : bond 0.04030 / 2.71 ( 757) hydrogen bonds : angle 4.82056 / 3.51 ( 2116) metal coordination : bond 0.00609 / 0.39 ( 12) metal coordination : angle 5.47549 / 3.51 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 623 TYR cc_start: 0.6921 (t80) cc_final: 0.6311 (t80) REVERT: A 339 MET cc_start: 0.8127 (ptt) cc_final: 0.7715 (ptp) REVERT: A 447 MET cc_start: 0.3079 (mpp) cc_final: 0.1792 (mmm) REVERT: A 706 MET cc_start: 0.2774 (tpt) cc_final: 0.2221 (tpt) outliers start: 34 outliers final: 33 residues processed: 215 average time/residue: 0.1233 time to fit residues: 42.6770 Evaluate side-chains 216 residues out of total 1865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 688 GLU Chi-restraints excluded: chain C residue 821 HIS Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1064 GLU Chi-restraints excluded: chain C residue 1177 LEU Chi-restraints excluded: chain C residue 1241 ILE Chi-restraints excluded: chain C residue 1261 VAL Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 0.0270 chunk 216 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 973 HIS C1209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.163351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129102 restraints weight = 34943.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126232 restraints weight = 34989.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127559 restraints weight = 32527.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127919 restraints weight = 22777.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128032 restraints weight = 20805.452| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18323 Z= 0.128 Angle : 0.628 14.021 25008 Z= 0.305 Chirality : 0.044 0.296 2870 Planarity : 0.004 0.050 3076 Dihedral : 11.607 152.698 2960 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.93 % Allowed : 19.30 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2140 helix: 1.16 (0.19), residues: 761 sheet: -0.50 (0.25), residues: 436 loop : -1.80 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.047 0.001 TYR C1083 PHE 0.013 0.001 PHE C 777 TRP 0.010 0.001 TRP C 658 HIS 0.013 0.001 HIS C 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (18311) covalent geometry : angle 0.61163 / 0.30 (24990) hydrogen bonds : bond 0.03919 / 2.64 ( 757) hydrogen bonds : angle 4.78148 / 3.47 ( 2116) metal coordination : bond 0.00568 / 0.37 ( 12) metal coordination : angle 5.35945 / 3.43 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.87 seconds wall clock time: 46 minutes 7.54 seconds (2767.54 seconds total)