Starting phenix.real_space_refine on Tue Sep 15 15:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199.map" model { file = "/net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7en1_31199/09_2026/7en1_31199_neut_trim.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 12880 2.51 5 N 3772 2.21 5 O 3716 1.98 5 H 20419 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 20280 Classifications: {'peptide': 1320} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1235} Chain breaks: 1 Chain: "B" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 71 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'J9F': 1, 'PNS': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'J9F:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {' MG': 1, 'AMP%rna2p': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA_mixed': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 6.54, per 1000 atoms: 0.16 Number of scatterers: 40862 At special positions: 0 Unit cell: (133, 148, 137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 69 16.00 P 4 15.00 Mg 2 11.99 O 3716 8.00 N 3772 7.00 C 12880 6.00 H 20419 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 24 sheets defined 47.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 240 through 257 removed outlier: 4.135A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 268 through 280 removed outlier: 3.948A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.802A pdb=" N ILE A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 343 through 360 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.016A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 457 through 464 removed outlier: 3.723A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 Processing helix chain 'A' and resid 534 through 546 removed outlier: 3.590A pdb=" N GLN A 538 " --> pdb=" O PRO A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 582 through 599 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 639 through 650 Processing helix chain 'A' and resid 670 through 676 Processing helix chain 'A' and resid 711 through 726 removed outlier: 4.319A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.774A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 762 through 766 Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 787 through 796 removed outlier: 3.551A pdb=" N LEU A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 4.658A pdb=" N GLY A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 906 through 913 Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.771A pdb=" N ALA A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 6.706A pdb=" N LEU A1031 " --> pdb=" O GLU A1028 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1048 removed outlier: 4.367A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1064 removed outlier: 3.910A pdb=" N ARG A1061 " --> pdb=" O ASP A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 Processing helix chain 'A' and resid 1089 through 1093 Processing helix chain 'A' and resid 1097 through 1103 Processing helix chain 'A' and resid 1107 through 1117 Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1138 through 1145 removed outlier: 3.522A pdb=" N GLY A1144 " --> pdb=" O TRP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1161 through 1172 removed outlier: 4.126A pdb=" N LEU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1185 Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1208 through 1219 Processing helix chain 'A' and resid 1235 through 1246 Processing helix chain 'A' and resid 1248 through 1252 removed outlier: 3.640A pdb=" N ARG A1251 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1265 Processing helix chain 'A' and resid 1291 through 1303 Processing helix chain 'A' and resid 1304 through 1308 Processing helix chain 'A' and resid 1327 through 1339 Processing helix chain 'A' and resid 1353 through 1368 Processing helix chain 'A' and resid 1377 through 1382 Processing helix chain 'A' and resid 1384 through 1399 removed outlier: 3.589A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1413 through 1423 removed outlier: 4.667A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1421 " --> pdb=" O LEU A1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.692A pdb=" N CYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.779A pdb=" N GLY B 119 " --> pdb=" O TRP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 188 through 206 removed outlier: 3.525A pdb=" N HIS B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 268 through 295 removed outlier: 4.781A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 343 through 360 Processing helix chain 'B' and resid 378 through 384 Processing helix chain 'B' and resid 403 through 422 removed outlier: 4.381A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 504 through 523 Processing helix chain 'B' and resid 534 through 546 Processing helix chain 'B' and resid 557 through 567 Processing helix chain 'B' and resid 582 through 599 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.731A pdb=" N GLY B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.898A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.754A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 768 through 780 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.589A pdb=" N LEU B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 797 " --> pdb=" O MET B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 826 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.620A pdb=" N GLY B 845 " --> pdb=" O THR B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 914 Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 1008 through 1027 removed outlier: 4.156A pdb=" N ALA B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 6.474A pdb=" N LEU B1031 " --> pdb=" O GLU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1048 removed outlier: 3.589A pdb=" N ASP B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1064 removed outlier: 3.876A pdb=" N ARG B1061 " --> pdb=" O ASP B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1083 Processing helix chain 'B' and resid 1087 through 1093 removed outlier: 4.261A pdb=" N ASP B1093 " --> pdb=" O LEU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1103 Processing helix chain 'B' and resid 1107 through 1116 removed outlier: 3.897A pdb=" N ARG B1114 " --> pdb=" O GLU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1125 Processing helix chain 'B' and resid 1140 through 1143 Processing helix chain 'B' and resid 1144 through 1149 Processing helix chain 'B' and resid 1161 through 1170 removed outlier: 4.094A pdb=" N LEU B1165 " --> pdb=" O SER B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1185 Processing helix chain 'B' and resid 1189 through 1191 No H-bonds generated for 'chain 'B' and resid 1189 through 1191' Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1208 through 1219 removed outlier: 3.722A pdb=" N GLY B1212 " --> pdb=" O ALA B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1246 Processing helix chain 'B' and resid 1248 through 1252 Processing helix chain 'B' and resid 1254 through 1265 Processing helix chain 'B' and resid 1291 through 1303 Processing helix chain 'B' and resid 1327 through 1340 removed outlier: 3.724A pdb=" N GLY B1340 " --> pdb=" O THR B1336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 325 removed outlier: 3.943A pdb=" N ARG A 485 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 372 Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.734A pdb=" N ALA A 572 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 733 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 785 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TRP A 784 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER A 813 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 786 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 810 " --> pdb=" O HIS A 836 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU A 838 " --> pdb=" O VAL A 810 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 812 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 867 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.309A pdb=" N VAL A 607 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA A 606 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 656 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU A 608 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 655 " --> pdb=" O LEU A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.742A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 902 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 877 removed outlier: 4.790A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 894 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 925 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY A 896 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR A 923 " --> pdb=" O GLY A 896 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 872 through 877 removed outlier: 4.790A pdb=" N ASP A 927 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE A 894 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 925 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLY A 896 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR A 923 " --> pdb=" O GLY A 896 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 941 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 930 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE A 939 " --> pdb=" O ARG A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.631A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 969 through 976 removed outlier: 3.635A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 984 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TRP A1313 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 986 " --> pdb=" O TRP A1313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1176 through 1180 removed outlier: 8.238A pdb=" N VAL A1177 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A1155 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN A1179 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A1157 " --> pdb=" O GLN A1179 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A1129 " --> pdb=" O ARG A1196 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE A1198 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A1131 " --> pdb=" O ILE A1198 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N PHE A1200 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A1195 " --> pdb=" O GLN A1223 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A1280 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 318 through 325 removed outlier: 6.319A pdb=" N VAL B 445 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU B 483 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 447 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG B 485 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASN B 449 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 364 through 372 Processing sheet with id=AB8, first strand: chain 'B' and resid 578 through 581 removed outlier: 6.775A pdb=" N ALA B 572 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 733 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG B 732 " --> pdb=" O LEU B 783 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASN B 785 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 734 " --> pdb=" O ASN B 785 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 784 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER B 813 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 786 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B 810 " --> pdb=" O HIS B 836 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 838 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 812 " --> pdb=" O LEU B 838 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 867 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.461A pdb=" N VAL B 607 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 654 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 655 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.785A pdb=" N GLY B 902 " --> pdb=" O GLU B 708 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 872 through 877 removed outlier: 5.040A pdb=" N ASP B 927 " --> pdb=" O LEU B 892 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG B 928 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 915 through 917 Processing sheet with id=AC4, first strand: chain 'B' and resid 946 through 949 Processing sheet with id=AC5, first strand: chain 'B' and resid 969 through 976 removed outlier: 6.648A pdb=" N LEU B 984 " --> pdb=" O ARG B1311 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP B1313 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 986 " --> pdb=" O TRP B1313 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1177 through 1178 removed outlier: 6.643A pdb=" N ARG B1129 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE B1198 " --> pdb=" O ARG B1129 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA B1131 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE B1200 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B1194 " --> pdb=" O ARG B1221 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN B1223 " --> pdb=" O TYR B1194 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG B1196 " --> pdb=" O GLN B1223 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG B1225 " --> pdb=" O ARG B1196 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE B1198 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B1227 " --> pdb=" O ILE B1198 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B1200 " --> pdb=" O LEU B1227 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B1229 " --> pdb=" O PHE B1200 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B1230 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1279 " --> pdb=" O ASP B1230 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B1280 " --> pdb=" O LEU B1272 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.83 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 7353 1.08 - 1.28: 16500 1.28 - 1.47: 7948 1.47 - 1.66: 9393 1.66 - 1.86: 94 Bond restraints: 41288 Sorted by residual: bond pdb=" N CYS A1505 " pdb=" H CYS A1505 " ideal model delta sigma weight residual 0.860 1.018 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" N CYS B1505 " pdb=" H CYS B1505 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C4 AMP A1504 " pdb=" C5 AMP A1504 " ideal model delta sigma weight residual 1.490 1.338 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N ALA A 794 " pdb=" H ALA A 794 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N TYR B 804 " pdb=" H TYR B 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 41283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.54: 74390 7.54 - 15.07: 302 15.07 - 22.61: 6 22.61 - 30.15: 0 30.15 - 37.68: 3 Bond angle restraints: 74701 Sorted by residual: angle pdb=" N GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 110.00 72.32 37.68 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 77.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CB GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 78.51 30.49 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CA PHE A 741 " pdb=" CB PHE A 741 " pdb=" CG PHE A 741 " ideal model delta sigma weight residual 113.80 122.27 -8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N PRO B 174 " pdb=" CA PRO B 174 " pdb=" CB PRO B 174 " ideal model delta sigma weight residual 103.22 107.09 -3.87 5.20e-01 3.70e+00 5.53e+01 ... (remaining 74696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 17521 21.16 - 42.33: 1083 42.33 - 63.49: 547 63.49 - 84.65: 118 84.65 - 105.82: 8 Dihedral angle restraints: 19277 sinusoidal: 10717 harmonic: 8560 Sorted by residual: dihedral pdb=" CA VAL A 486 " pdb=" C VAL A 486 " pdb=" N GLY A 487 " pdb=" CA GLY A 487 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA VAL B 486 " pdb=" C VAL B 486 " pdb=" N GLY B 487 " pdb=" CA GLY B 487 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER B 813 " pdb=" C SER B 813 " pdb=" N GLY B 814 " pdb=" CA GLY B 814 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2115 0.094 - 0.189: 886 0.189 - 0.283: 145 0.283 - 0.377: 28 0.377 - 0.472: 5 Chirality restraints: 3179 Sorted by residual: chirality pdb=" CA GLN B 689 " pdb=" N GLN B 689 " pdb=" C GLN B 689 " pdb=" CB GLN B 689 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP B 742 " pdb=" N ASP B 742 " pdb=" C ASP B 742 " pdb=" CB ASP B 742 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A1246 " pdb=" N ASP A1246 " pdb=" C ASP A1246 " pdb=" CB ASP A1246 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3176 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " 0.572 9.50e-02 1.11e+02 2.83e-01 1.02e+03 pdb=" NE ARG B 953 " 0.142 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.176 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.486 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.247 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.156 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.356 2.00e-02 2.50e+03 1.27e-01 6.43e+02 pdb=" CG TRP A 816 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.116 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.138 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 602 " -0.285 9.50e-02 1.11e+02 1.79e-01 5.24e+02 pdb=" NE ARG A 602 " -0.117 2.00e-02 2.50e+03 pdb=" CZ ARG A 602 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 602 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 602 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 602 " 0.261 2.00e-02 2.50e+03 pdb="HH12 ARG A 602 " -0.316 2.00e-02 2.50e+03 pdb="HH21 ARG A 602 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 602 " 0.149 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3002 2.16 - 2.77: 75789 2.77 - 3.38: 130085 3.38 - 3.99: 173450 3.99 - 4.60: 254695 Nonbonded interactions: 637021 Sorted by model distance: nonbonded pdb=" OE2 GLU A 608 " pdb=" HG SER A 610 " model vdw 1.552 2.450 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.572 2.450 nonbonded pdb=" OE1 GLU B1015 " pdb=" HG SER B1235 " model vdw 1.580 2.450 nonbonded pdb=" HG SER A 472 " pdb=" OD2 ASP A 480 " model vdw 1.586 2.450 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.593 2.450 ... (remaining 637016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 99 through 1340 or resid 1501 or resid 1503 through 1505)) \ selection = (chain 'B' and (resid 99 through 1501 or resid 1503 through 1504 or (resid 1505 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me H2 or name HA or name HB2 or name HB3 or name HG )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.260 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 42.480 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.013 0.155 20874 Z= 0.863 Angle : 1.971 21.372 28429 Z= 1.290 Chirality : 0.101 0.472 3179 Planarity : 0.022 0.206 3782 Dihedral : 15.119 105.818 7712 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.56 % Rotamer: Outliers : 1.72 % Allowed : 5.72 % Favored : 92.56 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.15), residues: 2648 helix: -1.68 (0.13), residues: 1092 sheet: -1.98 (0.24), residues: 422 loop : -0.97 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 953 TYR 0.205 0.034 TYR B 923 PHE 0.132 0.024 PHE B 372 TRP 0.229 0.035 TRP A 816 HIS 0.028 0.006 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.01285 / 0.84 (20869) covalent geometry : angle 1.97147 / 1.29 (28429) hydrogen bonds : bond 0.14432 / 9.57 ( 995) hydrogen bonds : angle 8.30724 / 5.96 ( 2796) Misc. bond : bond 0.12772 / 6.72 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.1741 (OUTLIER) cc_final: 0.1355 (t) REVERT: A 1073 MET cc_start: 0.5360 (mtp) cc_final: 0.4996 (mtm) REVERT: A 1207 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: B 715 ILE cc_start: 0.9224 (tp) cc_final: 0.8909 (tp) REVERT: B 1000 MET cc_start: 0.5895 (tmm) cc_final: 0.5600 (tmm) REVERT: B 1505 CYS cc_start: 0.5004 (m) cc_final: 0.4773 (m) outliers start: 35 outliers final: 10 residues processed: 266 average time/residue: 0.4880 time to fit residues: 180.2196 Evaluate side-chains 150 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN B 449 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.087817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063220 restraints weight = 188750.308| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.19 r_work: 0.3116 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 20874 Z= 0.297 Angle : 0.814 7.865 28429 Z= 0.419 Chirality : 0.043 0.429 3179 Planarity : 0.007 0.060 3782 Dihedral : 9.540 85.109 3039 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.58 % Allowed : 8.23 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.65 (0.16), residues: 2648 helix: -0.60 (0.14), residues: 1110 sheet: -1.99 (0.24), residues: 428 loop : -1.03 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1210 TYR 0.017 0.002 TYR A1194 PHE 0.021 0.003 PHE B 560 TRP 0.022 0.002 TRP B 535 HIS 0.008 0.002 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.30 (20869) covalent geometry : angle 0.81352 / 0.42 (28429) hydrogen bonds : bond 0.05783 / 3.84 ( 995) hydrogen bonds : angle 6.55621 / 4.74 ( 2796) Misc. bond : bond 0.00251 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.1477 (OUTLIER) cc_final: 0.1194 (t) REVERT: A 1073 MET cc_start: 0.4792 (mtp) cc_final: 0.4535 (mtm) REVERT: A 1207 GLU cc_start: 0.7925 (mp0) cc_final: 0.7721 (mm-30) REVERT: A 1219 LEU cc_start: 0.9066 (tp) cc_final: 0.8811 (tp) REVERT: B 346 SER cc_start: 0.8660 (m) cc_final: 0.8242 (p) REVERT: B 428 GLU cc_start: 0.8637 (tp30) cc_final: 0.8432 (mm-30) REVERT: B 924 ARG cc_start: 0.8590 (ttt-90) cc_final: 0.8246 (ttp80) REVERT: B 1000 MET cc_start: 0.6099 (tmm) cc_final: 0.5829 (tmm) REVERT: B 1335 MET cc_start: 0.8903 (mtm) cc_final: 0.8701 (mtm) REVERT: B 1505 CYS cc_start: 0.5947 (m) cc_final: 0.5556 (m) outliers start: 32 outliers final: 23 residues processed: 173 average time/residue: 0.4762 time to fit residues: 116.1895 Evaluate side-chains 144 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.087386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062108 restraints weight = 187440.397| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.07 r_work: 0.3111 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20874 Z= 0.244 Angle : 0.694 6.880 28429 Z= 0.358 Chirality : 0.040 0.399 3179 Planarity : 0.006 0.116 3782 Dihedral : 8.317 83.547 3025 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.53 % Allowed : 9.31 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2648 helix: -0.02 (0.15), residues: 1116 sheet: -2.21 (0.22), residues: 444 loop : -0.91 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1369 TYR 0.015 0.002 TYR A1194 PHE 0.022 0.002 PHE B1200 TRP 0.018 0.002 TRP B 535 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (20869) covalent geometry : angle 0.69412 / 0.36 (28429) hydrogen bonds : bond 0.04615 / 3.08 ( 995) hydrogen bonds : angle 6.02259 / 4.37 ( 2796) Misc. bond : bond 0.00131 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8853 (tt) REVERT: A 1055 SER cc_start: 0.1856 (OUTLIER) cc_final: 0.1517 (t) REVERT: A 1073 MET cc_start: 0.5106 (mtp) cc_final: 0.4881 (mtm) REVERT: A 1145 MET cc_start: 0.6513 (ttt) cc_final: 0.5368 (ppp) REVERT: A 1207 GLU cc_start: 0.7928 (mp0) cc_final: 0.7700 (mm-30) REVERT: A 1219 LEU cc_start: 0.9059 (tp) cc_final: 0.8856 (tp) REVERT: B 154 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (mm-40) REVERT: B 346 SER cc_start: 0.8571 (m) cc_final: 0.8207 (p) REVERT: B 428 GLU cc_start: 0.8689 (tp30) cc_final: 0.8445 (mm-30) REVERT: B 1073 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7595 (mtp) outliers start: 31 outliers final: 17 residues processed: 157 average time/residue: 0.4598 time to fit residues: 103.4594 Evaluate side-chains 139 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1170 THR Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 229 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.086691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.061349 restraints weight = 187672.795| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.08 r_work: 0.3092 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20874 Z= 0.266 Angle : 0.670 6.853 28429 Z= 0.344 Chirality : 0.040 0.402 3179 Planarity : 0.006 0.066 3782 Dihedral : 7.975 83.391 3023 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.53 % Allowed : 9.71 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.06 (0.16), residues: 2648 helix: 0.25 (0.15), residues: 1110 sheet: -2.30 (0.22), residues: 453 loop : -0.82 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.015 0.002 TYR A1194 PHE 0.017 0.002 PHE A1200 TRP 0.018 0.001 TRP B 535 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (20869) covalent geometry : angle 0.67049 / 0.34 (28429) hydrogen bonds : bond 0.04420 / 2.95 ( 995) hydrogen bonds : angle 5.87156 / 4.26 ( 2796) Misc. bond : bond 0.00142 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.9080 (mmm) cc_final: 0.8787 (mmp) REVERT: A 757 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 1055 SER cc_start: 0.1798 (OUTLIER) cc_final: 0.1516 (t) REVERT: A 1073 MET cc_start: 0.5031 (mtp) cc_final: 0.4801 (mtm) REVERT: A 1145 MET cc_start: 0.6624 (ttt) cc_final: 0.5465 (ppp) REVERT: A 1207 GLU cc_start: 0.7908 (mp0) cc_final: 0.7706 (mm-30) REVERT: B 346 SER cc_start: 0.8588 (m) cc_final: 0.8196 (p) REVERT: B 428 GLU cc_start: 0.8689 (tp30) cc_final: 0.8435 (mm-30) REVERT: B 708 GLU cc_start: 0.8322 (tt0) cc_final: 0.8113 (tt0) outliers start: 31 outliers final: 23 residues processed: 150 average time/residue: 0.4334 time to fit residues: 93.5031 Evaluate side-chains 139 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 250 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 239 optimal weight: 0.0670 chunk 195 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 421 HIS B 716 ASN B1223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.088506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066024 restraints weight = 186613.642| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.86 r_work: 0.3167 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20874 Z= 0.136 Angle : 0.610 6.164 28429 Z= 0.307 Chirality : 0.039 0.384 3179 Planarity : 0.005 0.055 3782 Dihedral : 7.520 83.496 3020 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.23 % Allowed : 10.25 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.71 (0.17), residues: 2648 helix: 0.61 (0.16), residues: 1117 sheet: -2.25 (0.22), residues: 455 loop : -0.64 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1210 TYR 0.021 0.002 TYR A1194 PHE 0.026 0.002 PHE B1200 TRP 0.019 0.001 TRP B 535 HIS 0.005 0.001 HIS B 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (20869) covalent geometry : angle 0.60970 / 0.31 (28429) hydrogen bonds : bond 0.03840 / 2.57 ( 995) hydrogen bonds : angle 5.61554 / 4.07 ( 2796) Misc. bond : bond 0.00059 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: A 849 ASN cc_start: 0.8184 (m110) cc_final: 0.7666 (m110) REVERT: A 865 TYR cc_start: 0.8655 (m-10) cc_final: 0.8228 (m-10) REVERT: A 1055 SER cc_start: 0.1859 (OUTLIER) cc_final: 0.1576 (t) REVERT: A 1073 MET cc_start: 0.5001 (mtp) cc_final: 0.4738 (mtm) REVERT: A 1145 MET cc_start: 0.6537 (ttt) cc_final: 0.5446 (ppp) REVERT: B 346 SER cc_start: 0.8598 (m) cc_final: 0.8322 (p) REVERT: B 924 ARG cc_start: 0.8746 (ttt-90) cc_final: 0.8353 (ttp80) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.4434 time to fit residues: 97.1929 Evaluate side-chains 138 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1321 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 161 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 211 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.088937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067031 restraints weight = 186394.347| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.83 r_work: 0.3194 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20874 Z= 0.120 Angle : 0.584 5.997 28429 Z= 0.291 Chirality : 0.038 0.385 3179 Planarity : 0.005 0.053 3782 Dihedral : 7.319 87.109 3020 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.28 % Allowed : 10.60 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2648 helix: 0.91 (0.16), residues: 1118 sheet: -2.15 (0.22), residues: 456 loop : -0.48 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.014 0.002 TYR B 272 PHE 0.016 0.002 PHE B1200 TRP 0.018 0.001 TRP B 535 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (20869) covalent geometry : angle 0.58372 / 0.29 (28429) hydrogen bonds : bond 0.03585 / 2.40 ( 995) hydrogen bonds : angle 5.40617 / 3.91 ( 2796) Misc. bond : bond 0.00060 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: A 849 ASN cc_start: 0.7989 (m110) cc_final: 0.7586 (m110) REVERT: A 865 TYR cc_start: 0.8557 (m-10) cc_final: 0.8050 (m-10) REVERT: A 1055 SER cc_start: 0.1917 (OUTLIER) cc_final: 0.1627 (t) REVERT: A 1073 MET cc_start: 0.4982 (mtp) cc_final: 0.4706 (mtm) REVERT: A 1145 MET cc_start: 0.6450 (ttt) cc_final: 0.5312 (ppp) REVERT: B 346 SER cc_start: 0.8584 (m) cc_final: 0.8292 (p) REVERT: B 511 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 736 VAL cc_start: 0.9609 (m) cc_final: 0.9307 (p) REVERT: B 924 ARG cc_start: 0.8667 (ttt-90) cc_final: 0.8315 (ttp80) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.4375 time to fit residues: 94.6710 Evaluate side-chains 134 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 228 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.086494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064056 restraints weight = 188775.060| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.06 r_work: 0.3085 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20874 Z= 0.208 Angle : 0.606 5.934 28429 Z= 0.305 Chirality : 0.038 0.394 3179 Planarity : 0.005 0.086 3782 Dihedral : 7.108 83.654 3013 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.43 % Allowed : 10.89 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.41 (0.17), residues: 2648 helix: 0.96 (0.16), residues: 1120 sheet: -2.26 (0.21), residues: 476 loop : -0.47 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.013 0.002 TYR B 272 PHE 0.014 0.002 PHE B 372 TRP 0.014 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (20869) covalent geometry : angle 0.60604 / 0.30 (28429) hydrogen bonds : bond 0.03757 / 2.50 ( 995) hydrogen bonds : angle 5.43341 / 3.93 ( 2796) Misc. bond : bond 0.00126 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: A 849 ASN cc_start: 0.7818 (m110) cc_final: 0.7375 (m110) REVERT: A 865 TYR cc_start: 0.8398 (m-10) cc_final: 0.7848 (m-10) REVERT: A 1055 SER cc_start: 0.1835 (OUTLIER) cc_final: 0.1567 (t) REVERT: A 1073 MET cc_start: 0.4945 (mtp) cc_final: 0.4691 (mtm) REVERT: A 1145 MET cc_start: 0.6545 (ttt) cc_final: 0.5411 (ppp) REVERT: B 346 SER cc_start: 0.8534 (m) cc_final: 0.8219 (p) REVERT: B 736 VAL cc_start: 0.9587 (m) cc_final: 0.9334 (p) REVERT: B 924 ARG cc_start: 0.8671 (ttt-90) cc_final: 0.8235 (ttp80) outliers start: 29 outliers final: 22 residues processed: 143 average time/residue: 0.4337 time to fit residues: 88.7177 Evaluate side-chains 134 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 240 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.085598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063141 restraints weight = 189129.766| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.19 r_work: 0.3058 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20874 Z= 0.250 Angle : 0.625 6.385 28429 Z= 0.316 Chirality : 0.039 0.394 3179 Planarity : 0.005 0.051 3782 Dihedral : 7.091 83.994 3013 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.48 % Allowed : 11.24 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.17), residues: 2648 helix: 0.90 (0.16), residues: 1124 sheet: -2.41 (0.21), residues: 483 loop : -0.53 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.013 0.002 TYR A1194 PHE 0.019 0.002 PHE A1200 TRP 0.013 0.001 TRP B 535 HIS 0.005 0.001 HIS B 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (20869) covalent geometry : angle 0.62491 / 0.32 (28429) hydrogen bonds : bond 0.03857 / 2.56 ( 995) hydrogen bonds : angle 5.47902 / 3.96 ( 2796) Misc. bond : bond 0.00139 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: A 946 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: A 1055 SER cc_start: 0.1727 (OUTLIER) cc_final: 0.1473 (t) REVERT: A 1073 MET cc_start: 0.4922 (mtp) cc_final: 0.4668 (mtm) REVERT: A 1145 MET cc_start: 0.6654 (ttt) cc_final: 0.5503 (ppp) REVERT: B 346 SER cc_start: 0.8764 (m) cc_final: 0.8457 (p) outliers start: 30 outliers final: 26 residues processed: 137 average time/residue: 0.4488 time to fit residues: 87.7971 Evaluate side-chains 131 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 946 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 101 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 239 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064071 restraints weight = 189445.627| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.16 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20874 Z= 0.170 Angle : 0.591 5.997 28429 Z= 0.295 Chirality : 0.038 0.384 3179 Planarity : 0.005 0.059 3782 Dihedral : 6.976 84.597 3013 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.13 % Allowed : 12.03 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.36 (0.17), residues: 2648 helix: 1.05 (0.16), residues: 1122 sheet: -2.39 (0.21), residues: 473 loop : -0.43 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.019 0.002 TYR B 865 PHE 0.015 0.002 PHE A1200 TRP 0.016 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (20869) covalent geometry : angle 0.59087 / 0.30 (28429) hydrogen bonds : bond 0.03600 / 2.41 ( 995) hydrogen bonds : angle 5.38059 / 3.88 ( 2796) Misc. bond : bond 0.00088 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8588 (pt0) REVERT: A 1055 SER cc_start: 0.1764 (OUTLIER) cc_final: 0.1524 (t) REVERT: A 1073 MET cc_start: 0.4828 (mtp) cc_final: 0.4567 (mtm) REVERT: A 1145 MET cc_start: 0.6585 (ttt) cc_final: 0.5499 (ppp) REVERT: B 346 SER cc_start: 0.8677 (m) cc_final: 0.8399 (p) REVERT: B 736 VAL cc_start: 0.9609 (m) cc_final: 0.9328 (p) outliers start: 23 outliers final: 21 residues processed: 132 average time/residue: 0.4598 time to fit residues: 87.0836 Evaluate side-chains 126 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1159 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 147 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 237 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064274 restraints weight = 188346.945| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.95 r_work: 0.3114 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20874 Z= 0.162 Angle : 0.586 5.799 28429 Z= 0.292 Chirality : 0.038 0.384 3179 Planarity : 0.005 0.050 3782 Dihedral : 6.885 83.843 3013 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.13 % Allowed : 12.07 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.30 (0.17), residues: 2648 helix: 1.11 (0.16), residues: 1129 sheet: -2.37 (0.21), residues: 471 loop : -0.43 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.016 0.002 TYR B 865 PHE 0.013 0.002 PHE B 560 TRP 0.016 0.001 TRP B 535 HIS 0.006 0.001 HIS A1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (20869) covalent geometry : angle 0.58605 / 0.29 (28429) hydrogen bonds : bond 0.03509 / 2.35 ( 995) hydrogen bonds : angle 5.31058 / 3.83 ( 2796) Misc. bond : bond 0.00081 / 0.04 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: A 1055 SER cc_start: 0.1866 (OUTLIER) cc_final: 0.1614 (t) REVERT: A 1073 MET cc_start: 0.4842 (mtp) cc_final: 0.4575 (mtm) REVERT: A 1145 MET cc_start: 0.6519 (ttt) cc_final: 0.5439 (ppp) REVERT: B 50 MET cc_start: 0.8879 (mtp) cc_final: 0.8641 (mtp) REVERT: B 346 SER cc_start: 0.8710 (m) cc_final: 0.8407 (p) REVERT: B 736 VAL cc_start: 0.9591 (m) cc_final: 0.9307 (p) REVERT: B 924 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8372 (ttp80) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.4854 time to fit residues: 89.3521 Evaluate side-chains 127 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1159 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 153 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.062412 restraints weight = 189103.095| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.17 r_work: 0.3115 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20874 Z= 0.126 Angle : 0.571 5.836 28429 Z= 0.282 Chirality : 0.038 0.379 3179 Planarity : 0.005 0.052 3782 Dihedral : 6.757 83.253 3013 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.99 % Allowed : 12.37 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -0.16 (0.17), residues: 2648 helix: 1.22 (0.16), residues: 1130 sheet: -2.33 (0.21), residues: 473 loop : -0.33 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.013 0.002 TYR B 865 PHE 0.014 0.001 PHE B 372 TRP 0.017 0.001 TRP B 535 HIS 0.009 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20869) covalent geometry : angle 0.57091 / 0.28 (28429) hydrogen bonds : bond 0.03320 / 2.22 ( 995) hydrogen bonds : angle 5.19623 / 3.74 ( 2796) Misc. bond : bond 0.00051 / 0.03 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9112.41 seconds wall clock time: 155 minutes 9.16 seconds (9309.16 seconds total)