Starting phenix.real_space_refine on Fri Mar 6 07:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.map" model { file = "/net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ric_4888/03_2026/6ric_4888.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 Mg 1 5.21 5 S 136 5.16 5 C 19079 2.51 5 N 4926 2.21 5 O 5531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29677 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 10071 Classifications: {'peptide': 1254} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1210} Chain breaks: 2 Chain: "B" Number of atoms: 8991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8991 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1065} Chain breaks: 5 Chain: "C" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2475 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 8, 'TRANS': 175} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 849 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "G" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "I" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3241 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 4 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 58} Chain: "S" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1036 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 360 SG CYS A 49 42.342 96.300 104.792 1.00 76.90 S ATOM 382 SG CYS A 52 42.158 100.011 104.469 1.00 76.24 S ATOM 434 SG CYS A 59 44.247 98.550 102.025 1.00 70.98 S ATOM 694 SG CYS A 90 85.908 80.211 118.549 1.00 58.96 S ATOM 718 SG CYS A 93 86.199 82.282 121.392 1.00 54.54 S ATOM 1016 SG CYS A 130 88.806 82.154 120.170 1.00 75.08 S ATOM 1059 SG CYS A 135 86.760 79.053 122.200 1.00 66.32 S ATOM 18471 SG CYS B1087 56.731 106.118 109.825 1.00 65.04 S ATOM 18494 SG CYS B1090 56.778 102.999 109.806 1.00 64.98 S ATOM 18583 SG CYS B1103 53.832 103.280 110.439 1.00 64.18 S ATOM 18608 SG CYS B1106 56.957 103.678 112.694 1.00 59.66 S ATOM 28194 SG CYS J 7 41.982 98.820 31.606 1.00 36.99 S ATOM 28213 SG CYS J 10 41.164 101.876 29.227 1.00 39.06 S ATOM 28450 SG CYS J 39 44.645 100.542 29.558 1.00 39.65 S ATOM 28456 SG CYS J 40 41.588 99.348 27.951 1.00 40.29 S Time building chain proxies: 6.15, per 1000 atoms: 0.21 Number of scatterers: 29677 At special positions: 0 Unit cell: (152.28, 160.38, 154.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 136 16.00 Mg 1 11.99 O 5531 8.00 N 4926 7.00 C 19079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A 62 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 49 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 52 " pdb=" ZN A1303 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 93 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 135 " pdb="ZN ZN A1303 " - pdb=" SG CYS A 90 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1103 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1090 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1106 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1087 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 39 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 40 " Number of angles added : 21 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7002 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 47 sheets defined 39.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 38 through 42 removed outlier: 3.743A pdb=" N GLY A 42 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.713A pdb=" N GLU A 58 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 59 " --> pdb=" O GLU A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 59' Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.518A pdb=" N ILE A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 4.317A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.658A pdb=" N GLN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.515A pdb=" N TRP A 177 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.502A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.704A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.558A pdb=" N ILE A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.535A pdb=" N TYR A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 265 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.549A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 458 through 470 removed outlier: 4.005A pdb=" N VAL A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.503A pdb=" N TYR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.774A pdb=" N PHE A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 550 through 572 removed outlier: 3.501A pdb=" N PHE A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.603A pdb=" N LEU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 615 removed outlier: 3.537A pdb=" N ASN A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 656 removed outlier: 3.632A pdb=" N ILE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 removed outlier: 3.516A pdb=" N ALA A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.981A pdb=" N TYR A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 700 removed outlier: 3.534A pdb=" N ARG A 700 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 727 through 764 removed outlier: 3.762A pdb=" N PHE A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 809 through 821 removed outlier: 3.669A pdb=" N LYS A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.094A pdb=" N VAL A 844 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 875 removed outlier: 3.560A pdb=" N ASP A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 873 " --> pdb=" O ASP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.537A pdb=" N GLU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.717A pdb=" N THR A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 943 Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 984 through 996 removed outlier: 4.057A pdb=" N LEU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1004 removed outlier: 3.707A pdb=" N ASN A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1001 through 1004' Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.609A pdb=" N PHE A1044 " --> pdb=" O MET A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1093 removed outlier: 3.686A pdb=" N VAL A1088 " --> pdb=" O LYS A1084 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.616A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 removed outlier: 3.572A pdb=" N LEU A1133 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A1135 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A1136 " --> pdb=" O LEU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1155 through 1170 removed outlier: 3.515A pdb=" N THR A1170 " --> pdb=" O ALA A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1207 through 1216 removed outlier: 4.026A pdb=" N ASP A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1234 through 1239 Processing helix chain 'A' and resid 1258 through 1263 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.607A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.520A pdb=" N HIS B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.518A pdb=" N GLY B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 260 through 278 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.796A pdb=" N ALA B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 313 removed outlier: 4.058A pdb=" N GLU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.539A pdb=" N ASN B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 344 removed outlier: 3.908A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.604A pdb=" N HIS B 357 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 384 removed outlier: 3.578A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.762A pdb=" N SER B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.520A pdb=" N LEU B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.557A pdb=" N ILE B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.949A pdb=" N THR B 550 " --> pdb=" O CYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.568A pdb=" N PHE B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 649 Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.671A pdb=" N ASP B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 683 through 695 removed outlier: 3.995A pdb=" N ALA B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 731 removed outlier: 4.117A pdb=" N GLU B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 730 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.507A pdb=" N ARG B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.534A pdb=" N ASN B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 788' Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.572A pdb=" N LEU B 902 " --> pdb=" O GLU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 923 removed outlier: 3.509A pdb=" N PHE B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 941 Processing helix chain 'B' and resid 961 through 977 Processing helix chain 'B' and resid 981 through 990 Processing helix chain 'B' and resid 1054 through 1064 removed outlier: 3.545A pdb=" N LEU B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1075 Processing helix chain 'B' and resid 1103 through 1109 removed outlier: 3.792A pdb=" N LYS B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1133 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.566A pdb=" N TRP C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 5.353A pdb=" N MET C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.582A pdb=" N ASN C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 207 through 230 removed outlier: 3.852A pdb=" N CYS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.657A pdb=" N PHE C 265 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.665A pdb=" N TYR E 8 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.925A pdb=" N ILE E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 78 through 95 Processing helix chain 'F' and resid 112 through 123 removed outlier: 3.680A pdb=" N VAL F 116 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.584A pdb=" N LEU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 107 through 119 removed outlier: 3.589A pdb=" N LEU I 114 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 169 No H-bonds generated for 'chain 'I' and resid 167 through 169' Processing helix chain 'I' and resid 170 through 178 Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 255 through 261 removed outlier: 3.781A pdb=" N LYS I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 267 removed outlier: 4.352A pdb=" N LEU I 266 " --> pdb=" O VAL I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 279 Processing helix chain 'I' and resid 283 through 285 No H-bonds generated for 'chain 'I' and resid 283 through 285' Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.681A pdb=" N ILE I 291 " --> pdb=" O TYR I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 650 removed outlier: 3.611A pdb=" N LEU I 642 " --> pdb=" O THR I 638 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS I 643 " --> pdb=" O ASP I 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I 647 " --> pdb=" O LYS I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 689 through 691 No H-bonds generated for 'chain 'I' and resid 689 through 691' Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 723 through 742 removed outlier: 3.517A pdb=" N ILE I 736 " --> pdb=" O ASN I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 769 removed outlier: 3.575A pdb=" N LEU I 760 " --> pdb=" O ASN I 756 " (cutoff:3.500A) Processing helix chain 'I' and resid 773 through 792 removed outlier: 5.983A pdb=" N THR I 783 " --> pdb=" O ASP I 779 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG I 784 " --> pdb=" O GLU I 780 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU I 787 " --> pdb=" O THR I 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.527A pdb=" N TYR J 19 " --> pdb=" O SER J 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS J 20 " --> pdb=" O HIS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 32 Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'S' and resid 24 through 29 Processing helix chain 'S' and resid 37 through 48 removed outlier: 3.750A pdb=" N GLU S 42 " --> pdb=" O GLU S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 81 removed outlier: 3.668A pdb=" N ILE S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY S 75 " --> pdb=" O LYS S 71 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 85 removed outlier: 3.563A pdb=" N LYS S 85 " --> pdb=" O SER S 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 82 through 85' Processing helix chain 'S' and resid 114 through 131 removed outlier: 3.585A pdb=" N LYS S 126 " --> pdb=" O LEU S 122 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE S 128 " --> pdb=" O GLY S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 1229 through 1231 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 4.316A pdb=" N SER A 67 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.979A pdb=" N PHE A 151 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 158 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 282 removed outlier: 3.812A pdb=" N ILE B1051 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1027 through 1029 removed outlier: 7.401A pdb=" N ILE A 402 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 289 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE A 404 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLY A 291 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 7.129A pdb=" N ALA A 369 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 334 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 518 through 519 Processing sheet with id=AB1, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.393A pdb=" N VAL A 774 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 796 through 799 Processing sheet with id=AB4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AB5, first strand: chain 'A' and resid 1106 through 1111 Processing sheet with id=AB6, first strand: chain 'A' and resid 998 through 999 Processing sheet with id=AB7, first strand: chain 'A' and resid 1006 through 1011 removed outlier: 3.628A pdb=" N ILE A1021 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 138 removed outlier: 3.612A pdb=" N LYS A1253 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1264 through 1265 Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.611A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.611A pdb=" N ILE B 66 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 58 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 64 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL B 73 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 97 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 75 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 95 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC5, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.646A pdb=" N VAL B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC7, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC8, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AC9, first strand: chain 'B' and resid 535 through 540 removed outlier: 5.514A pdb=" N LEU B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 532 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 538 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE B 580 " --> pdb=" O PRO B 529 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR B 531 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.270A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 removed outlier: 6.270A pdb=" N MET B 872 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL B 854 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLU B 874 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N SER B 852 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 723 through 724 Processing sheet with id=AD4, first strand: chain 'B' and resid 992 through 993 removed outlier: 6.773A pdb=" N ILE B 758 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL B 896 " --> pdb=" O ILE B 758 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 760 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N VAL B 913 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR B 743 " --> pdb=" O VAL B 913 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE B 915 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA B 745 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B1009 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1084 through 1087 removed outlier: 4.347A pdb=" N VAL B1084 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 5 through 13 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AD9, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.558A pdb=" N ILE C 37 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN C 43 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C 138 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AE2, first strand: chain 'C' and resid 233 through 234 removed outlier: 6.155A pdb=" N LYS C 233 " --> pdb=" O TYR C 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AE4, first strand: chain 'E' and resid 112 through 115 removed outlier: 4.308A pdb=" N SER E 112 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET E 142 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.215A pdb=" N LYS G 47 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA G 77 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA G 45 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS G 43 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 84 through 91 removed outlier: 6.050A pdb=" N ILE G 105 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA G 156 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS G 107 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE G 158 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL G 153 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA G 144 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU G 155 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 220 through 228 removed outlier: 3.520A pdb=" N ILE I 217 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP I 228 " --> pdb=" O VAL I 209 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 209 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET I 121 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU I 214 " --> pdb=" O MET I 121 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LEU I 123 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 10.919A pdb=" N LYS I 216 " --> pdb=" O LEU I 123 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR I 234 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.023A pdb=" N ILE I 130 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE I 166 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL I 132 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 664 through 665 removed outlier: 4.664A pdb=" N ILE I 658 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 669 through 670 1193 hydrogen bonds defined for protein. 3303 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: 8.90 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9251 1.34 - 1.46: 5168 1.46 - 1.57: 15634 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 30269 Sorted by residual: bond pdb=" C ILE I 264 " pdb=" N PRO I 265 " ideal model delta sigma weight residual 1.335 1.373 -0.037 1.30e-02 5.92e+03 8.31e+00 bond pdb=" CG1 ILE B 722 " pdb=" CD1 ILE B 722 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.19e+00 bond pdb=" CA PRO I 716 " pdb=" CB PRO I 716 " ideal model delta sigma weight residual 1.531 1.520 0.011 6.20e-03 2.60e+04 3.42e+00 bond pdb=" CB VAL A 534 " pdb=" CG1 VAL A 534 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CG1 ILE A1247 " pdb=" CD1 ILE A1247 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.00e+00 ... (remaining 30264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 40014 2.17 - 4.34: 790 4.34 - 6.50: 80 6.50 - 8.67: 18 8.67 - 10.84: 4 Bond angle restraints: 40906 Sorted by residual: angle pdb=" N GLN A 459 " pdb=" CA GLN A 459 " pdb=" C GLN A 459 " ideal model delta sigma weight residual 111.37 118.60 -7.23 1.65e+00 3.67e-01 1.92e+01 angle pdb=" C GLU B 533 " pdb=" N ASN B 534 " pdb=" CA ASN B 534 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" N GLY B1044 " pdb=" CA GLY B1044 " pdb=" C GLY B1044 " ideal model delta sigma weight residual 112.18 117.68 -5.50 1.34e+00 5.57e-01 1.69e+01 angle pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta sigma weight residual 120.82 126.86 -6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" N ASN G 63 " pdb=" CA ASN G 63 " pdb=" C ASN G 63 " ideal model delta sigma weight residual 110.80 118.53 -7.73 2.13e+00 2.20e-01 1.32e+01 ... (remaining 40901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 16425 17.23 - 34.47: 1616 34.47 - 51.70: 298 51.70 - 68.94: 40 68.94 - 86.17: 23 Dihedral angle restraints: 18402 sinusoidal: 7565 harmonic: 10837 Sorted by residual: dihedral pdb=" CA VAL G 62 " pdb=" C VAL G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta harmonic sigma weight residual 180.00 -140.16 -39.84 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA ILE A 458 " pdb=" C ILE A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual -180.00 -146.93 -33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ASN B 736 " pdb=" C ASN B 736 " pdb=" N CYS B 737 " pdb=" CA CYS B 737 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 18399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3980 0.075 - 0.149: 612 0.149 - 0.224: 44 0.224 - 0.298: 6 0.298 - 0.373: 1 Chirality restraints: 4643 Sorted by residual: chirality pdb=" CB ILE F 77 " pdb=" CA ILE F 77 " pdb=" CG1 ILE F 77 " pdb=" CG2 ILE F 77 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE I 161 " pdb=" CA ILE I 161 " pdb=" CG1 ILE I 161 " pdb=" CG2 ILE I 161 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 106 " pdb=" CA ILE A 106 " pdb=" CG1 ILE A 106 " pdb=" CG2 ILE A 106 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4640 not shown) Planarity restraints: 5165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 100 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 101 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 172 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO I 173 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO I 173 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 173 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 140 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO B 141 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.034 5.00e-02 4.00e+02 ... (remaining 5162 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 383 2.63 - 3.20: 24663 3.20 - 3.77: 47270 3.77 - 4.33: 71106 4.33 - 4.90: 112917 Nonbonded interactions: 256339 Sorted by model distance: nonbonded pdb=" OD1 ASP A 417 " pdb="MG MG A1301 " model vdw 2.068 2.170 nonbonded pdb=" OG SER A 145 " pdb=" O LYS A 148 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 673 " pdb=" OG SER B 956 " model vdw 2.258 3.040 nonbonded pdb=" O ARG B 249 " pdb=" OG SER B 253 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 309 " pdb=" OE2 GLU I 725 " model vdw 2.266 3.040 ... (remaining 256334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.490 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: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.960 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.006 0.091 30285 Z= 0.242 Angle : 0.843 30.902 40927 Z= 0.423 Chirality : 0.053 0.373 4643 Planarity : 0.006 0.067 5165 Dihedral : 14.009 86.175 11400 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.16 (0.11), residues: 3619 helix: -4.19 (0.06), residues: 1314 sheet: -1.83 (0.20), residues: 512 loop : -1.77 (0.12), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 203 TYR 0.025 0.002 TYR E 8 PHE 0.042 0.002 PHE A 938 TRP 0.018 0.002 TRP A 809 HIS 0.011 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00565 (30269) covalent geometry : angle 0.75432 (40906) hydrogen bonds : bond 0.26630 ( 1152) hydrogen bonds : angle 9.93720 ( 3303) metal coordination : bond 0.05983 ( 16) metal coordination : angle 16.62892 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 710 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: A 497 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8409 (ttpp) REVERT: A 705 TYR cc_start: 0.8465 (m-80) cc_final: 0.8260 (m-80) REVERT: A 853 ASN cc_start: 0.8048 (t0) cc_final: 0.7826 (t0) REVERT: A 974 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8281 (ttmm) REVERT: A 1043 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7631 (ttm110) REVERT: A 1218 LYS cc_start: 0.8269 (mptt) cc_final: 0.7415 (mppt) REVERT: A 1222 ASN cc_start: 0.8350 (m110) cc_final: 0.7850 (m110) REVERT: B 23 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8450 (mmtm) REVERT: B 501 GLU cc_start: 0.7687 (pt0) cc_final: 0.7485 (pt0) REVERT: B 555 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8251 (mtp85) REVERT: B 804 ASN cc_start: 0.7983 (m110) cc_final: 0.7699 (m-40) REVERT: B 987 ASP cc_start: 0.8058 (m-30) cc_final: 0.7716 (m-30) REVERT: B 1025 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8424 (mtpt) REVERT: B 1034 LYS cc_start: 0.8052 (mttm) cc_final: 0.7842 (mttm) REVERT: B 1096 GLN cc_start: 0.7532 (mt0) cc_final: 0.7028 (mt0) REVERT: C 164 GLU cc_start: 0.7376 (mp0) cc_final: 0.7042 (mp0) REVERT: C 283 ASP cc_start: 0.7695 (t70) cc_final: 0.7097 (t70) REVERT: E 21 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7583 (ptp-170) REVERT: E 22 ASP cc_start: 0.7932 (t70) cc_final: 0.7662 (t0) REVERT: G 69 ASN cc_start: 0.8157 (m-40) cc_final: 0.7869 (m-40) REVERT: G 84 ILE cc_start: 0.8067 (mp) cc_final: 0.7623 (mm) REVERT: I 605 LYS cc_start: 0.8303 (tttt) cc_final: 0.6399 (ttmt) REVERT: I 660 VAL cc_start: 0.7772 (t) cc_final: 0.7438 (p) REVERT: I 703 ASN cc_start: 0.5904 (t0) cc_final: 0.5445 (t0) REVERT: J 62 ILE cc_start: 0.7433 (mt) cc_final: 0.7197 (mt) outliers start: 1 outliers final: 1 residues processed: 711 average time/residue: 0.7257 time to fit residues: 594.7284 Evaluate side-chains 478 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 686 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 137 GLN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 472 GLN A 513 ASN A 526 ASN A 548 HIS A 611 ASN A 660 ASN A 894 ASN A 941 GLN A 947 HIS ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN A1142 ASN B 169 ASN B 298 GLN B 318 HIS B 391 ASN B 481 GLN B 620 GLN B 682 ASN B 693 GLN B 740 GLN B 741 HIS B 778 HIS B 858 GLN B 977 ASN B1040 GLN B1089 ASN C 8 ASN C 24 GLN E 98 ASN F 112 ASN F 140 ASN G 29 ASN G 64 ASN I 271 HIS ** I 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 695 ASN ** J 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN S 90 ASN S 145 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106983 restraints weight = 37822.358| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.63 r_work: 0.3080 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30285 Z= 0.203 Angle : 0.623 14.343 40927 Z= 0.328 Chirality : 0.046 0.186 4643 Planarity : 0.005 0.044 5165 Dihedral : 5.383 33.258 3996 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 12.71 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.18 (0.12), residues: 3619 helix: -1.72 (0.12), residues: 1315 sheet: -1.43 (0.20), residues: 524 loop : -1.09 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 659 TYR 0.022 0.002 TYR A 732 PHE 0.038 0.002 PHE A 938 TRP 0.017 0.002 TRP A 365 HIS 0.011 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00477 (30269) covalent geometry : angle 0.61283 (40906) hydrogen bonds : bond 0.04486 ( 1152) hydrogen bonds : angle 5.45994 ( 3303) metal coordination : bond 0.01015 ( 16) metal coordination : angle 5.02578 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8687 (mt) cc_final: 0.8476 (mp) REVERT: A 68 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6669 (pt) REVERT: A 179 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 182 ILE cc_start: 0.8132 (mt) cc_final: 0.7891 (mm) REVERT: A 628 ASP cc_start: 0.8017 (t0) cc_final: 0.7616 (m-30) REVERT: A 650 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8009 (mtp180) REVERT: A 834 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8441 (mttp) REVERT: A 856 LYS cc_start: 0.7242 (mmmt) cc_final: 0.6998 (tppt) REVERT: A 974 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8179 (ttmm) REVERT: B 9 MET cc_start: 0.8628 (tpp) cc_final: 0.8401 (tpt) REVERT: B 67 MET cc_start: 0.5820 (mtm) cc_final: 0.5568 (mtm) REVERT: B 555 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8544 (mtp85) REVERT: B 720 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8119 (mtp-110) REVERT: B 804 ASN cc_start: 0.8277 (m110) cc_final: 0.8040 (m-40) REVERT: B 1034 LYS cc_start: 0.8386 (mttm) cc_final: 0.8168 (mttp) REVERT: B 1082 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: B 1096 GLN cc_start: 0.7751 (mt0) cc_final: 0.7282 (mt0) REVERT: B 1131 MET cc_start: 0.9006 (mmm) cc_final: 0.8641 (mmm) REVERT: E 21 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.8052 (ptp-170) REVERT: E 22 ASP cc_start: 0.8279 (t70) cc_final: 0.8063 (t0) REVERT: G 15 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8075 (mm-30) REVERT: G 55 GLU cc_start: 0.7886 (tp30) cc_final: 0.7624 (tp30) REVERT: G 84 ILE cc_start: 0.8385 (mp) cc_final: 0.7674 (mm) REVERT: G 107 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7202 (pttp) REVERT: I 189 LEU cc_start: 0.6952 (tp) cc_final: 0.6367 (pt) REVERT: I 215 TYR cc_start: 0.7084 (t80) cc_final: 0.6872 (t80) REVERT: I 216 LYS cc_start: 0.6555 (mmmt) cc_final: 0.6186 (tppp) REVERT: I 242 LYS cc_start: 0.7730 (mttp) cc_final: 0.7523 (ptpp) REVERT: I 268 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7451 (tppt) REVERT: I 659 ARG cc_start: 0.6380 (mtp85) cc_final: 0.5878 (mmt90) REVERT: I 660 VAL cc_start: 0.7762 (t) cc_final: 0.7294 (p) outliers start: 90 outliers final: 29 residues processed: 555 average time/residue: 0.6801 time to fit residues: 438.2357 Evaluate side-chains 488 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 453 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 1082 GLN Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 82 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 225 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 360 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 611 ASN A 894 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 971 GLN B 977 ASN B1089 ASN C 24 GLN C 229 ASN E 98 ASN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN G 7 ASN G 29 ASN ** I 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN S 90 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110175 restraints weight = 37901.528| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.63 r_work: 0.3140 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30285 Z= 0.113 Angle : 0.534 11.216 40927 Z= 0.280 Chirality : 0.044 0.175 4643 Planarity : 0.004 0.039 5165 Dihedral : 4.848 25.315 3994 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 15.30 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -1.28 (0.13), residues: 3619 helix: -0.55 (0.13), residues: 1319 sheet: -1.14 (0.21), residues: 505 loop : -0.87 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 72 TYR 0.016 0.001 TYR A 732 PHE 0.031 0.001 PHE A 938 TRP 0.016 0.001 TRP A 365 HIS 0.006 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00254 (30269) covalent geometry : angle 0.52622 (40906) hydrogen bonds : bond 0.03770 ( 1152) hydrogen bonds : angle 4.90662 ( 3303) metal coordination : bond 0.00552 ( 16) metal coordination : angle 4.01277 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 499 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8659 (mt) cc_final: 0.8374 (mp) REVERT: A 68 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6729 (pt) REVERT: A 70 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7545 (mppt) REVERT: A 182 ILE cc_start: 0.8066 (mt) cc_final: 0.7840 (mm) REVERT: A 497 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8646 (ttpp) REVERT: A 555 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.9004 (mm) REVERT: A 628 ASP cc_start: 0.7974 (t0) cc_final: 0.7580 (m-30) REVERT: A 747 CYS cc_start: 0.8466 (t) cc_final: 0.8111 (m) REVERT: A 974 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8278 (ttmm) REVERT: A 1097 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8275 (mtmt) REVERT: B 231 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 297 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8322 (tppt) REVERT: B 408 ASN cc_start: 0.6590 (m-40) cc_final: 0.6165 (m110) REVERT: B 519 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 804 ASN cc_start: 0.8285 (m110) cc_final: 0.8036 (m-40) REVERT: B 1056 MET cc_start: 0.9113 (mtm) cc_final: 0.8880 (mtp) REVERT: B 1079 GLU cc_start: 0.7782 (pm20) cc_final: 0.7534 (mp0) REVERT: B 1082 GLN cc_start: 0.8285 (pm20) cc_final: 0.8048 (pt0) REVERT: B 1096 GLN cc_start: 0.7676 (mt0) cc_final: 0.7186 (mt0) REVERT: B 1102 THR cc_start: 0.8808 (p) cc_final: 0.8525 (t) REVERT: B 1131 MET cc_start: 0.9013 (mmm) cc_final: 0.8595 (mmm) REVERT: E 21 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.8027 (ptp-170) REVERT: G 52 GLU cc_start: 0.7558 (tp30) cc_final: 0.7202 (tm-30) REVERT: G 55 GLU cc_start: 0.7893 (tp30) cc_final: 0.7597 (tp30) REVERT: G 60 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7764 (mt-10) REVERT: I 112 TYR cc_start: 0.7134 (m-80) cc_final: 0.6877 (m-80) REVERT: I 189 LEU cc_start: 0.6996 (tp) cc_final: 0.6367 (pt) REVERT: I 215 TYR cc_start: 0.7132 (t80) cc_final: 0.6876 (t80) REVERT: I 242 LYS cc_start: 0.7616 (mttp) cc_final: 0.7412 (ptpp) REVERT: I 268 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7415 (tppt) REVERT: I 294 ASP cc_start: 0.7023 (m-30) cc_final: 0.6763 (m-30) REVERT: I 659 ARG cc_start: 0.6342 (mtp85) cc_final: 0.5916 (mmt90) REVERT: I 677 ILE cc_start: 0.6369 (OUTLIER) cc_final: 0.6157 (pp) REVERT: I 701 TYR cc_start: 0.6263 (m-80) cc_final: 0.5997 (m-80) REVERT: S 50 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8052 (ttmm) REVERT: S 70 SER cc_start: 0.8579 (t) cc_final: 0.8215 (m) outliers start: 82 outliers final: 27 residues processed: 541 average time/residue: 0.6609 time to fit residues: 418.3251 Evaluate side-chains 476 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 444 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 677 ILE Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 158 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 118 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 611 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 977 ASN B1042 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN F 112 ASN F 140 ASN G 7 ASN I 284 HIS J 53 ASN S 90 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108467 restraints weight = 37655.560| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.62 r_work: 0.3084 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30285 Z= 0.146 Angle : 0.543 11.530 40927 Z= 0.285 Chirality : 0.045 0.184 4643 Planarity : 0.004 0.040 5165 Dihedral : 4.735 25.748 3994 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.77 % Allowed : 16.49 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.83 (0.13), residues: 3619 helix: -0.03 (0.14), residues: 1323 sheet: -1.00 (0.22), residues: 503 loop : -0.71 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 720 TYR 0.020 0.001 TYR I 109 PHE 0.032 0.001 PHE A 938 TRP 0.011 0.001 TRP I 315 HIS 0.009 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00341 (30269) covalent geometry : angle 0.53634 (40906) hydrogen bonds : bond 0.03707 ( 1152) hydrogen bonds : angle 4.73414 ( 3303) metal coordination : bond 0.00688 ( 16) metal coordination : angle 3.78076 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 483 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6653 (pt) REVERT: A 70 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7379 (mppt) REVERT: A 182 ILE cc_start: 0.8111 (mt) cc_final: 0.7865 (mm) REVERT: A 333 GLN cc_start: 0.8653 (mt0) cc_final: 0.8364 (mt0) REVERT: A 555 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 628 ASP cc_start: 0.7961 (t0) cc_final: 0.7583 (m-30) REVERT: A 706 LEU cc_start: 0.9303 (mt) cc_final: 0.9086 (mp) REVERT: A 747 CYS cc_start: 0.8481 (t) cc_final: 0.8132 (m) REVERT: A 856 LYS cc_start: 0.7315 (mmmt) cc_final: 0.6959 (tppt) REVERT: A 974 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8332 (ttmm) REVERT: A 1053 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: A 1200 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8199 (mmtm) REVERT: B 54 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6562 (mtm110) REVERT: B 100 VAL cc_start: 0.7523 (t) cc_final: 0.7270 (m) REVERT: B 216 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: B 297 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8300 (tppt) REVERT: B 511 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7987 (tm-30) REVERT: B 519 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: B 720 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8004 (mtp-110) REVERT: B 1015 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8857 (t80) REVERT: B 1056 MET cc_start: 0.9124 (mtm) cc_final: 0.8873 (mtp) REVERT: B 1079 GLU cc_start: 0.7851 (pm20) cc_final: 0.7637 (mp0) REVERT: B 1096 GLN cc_start: 0.7690 (mt0) cc_final: 0.7236 (mt0) REVERT: B 1131 MET cc_start: 0.9002 (mmm) cc_final: 0.8646 (mmm) REVERT: E 21 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8015 (ptp-170) REVERT: E 177 ASP cc_start: 0.8733 (m-30) cc_final: 0.8464 (m-30) REVERT: G 55 GLU cc_start: 0.7916 (tp30) cc_final: 0.7501 (tp30) REVERT: G 60 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7844 (mt-10) REVERT: I 183 ARG cc_start: 0.5806 (mtt90) cc_final: 0.5484 (mtt180) REVERT: I 189 LEU cc_start: 0.6953 (tp) cc_final: 0.6377 (pt) REVERT: I 215 TYR cc_start: 0.7191 (t80) cc_final: 0.6970 (t80) REVERT: I 268 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7419 (tppt) REVERT: I 294 ASP cc_start: 0.6885 (m-30) cc_final: 0.6629 (m-30) REVERT: I 659 ARG cc_start: 0.6385 (mtp85) cc_final: 0.5924 (mmt90) REVERT: I 677 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6013 (pp) REVERT: I 701 TYR cc_start: 0.6302 (m-80) cc_final: 0.5866 (m-80) REVERT: S 70 SER cc_start: 0.8567 (t) cc_final: 0.8213 (m) outliers start: 93 outliers final: 33 residues processed: 533 average time/residue: 0.6640 time to fit residues: 413.6884 Evaluate side-chains 488 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 446 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 677 ILE Chi-restraints excluded: chain I residue 686 ILE Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 297 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 262 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 265 optimal weight: 5.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN A 611 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN F 112 ASN F 140 ASN G 7 ASN G 63 ASN ** I 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 HIS J 53 ASN S 90 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108159 restraints weight = 37677.014| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.63 r_work: 0.3098 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30285 Z= 0.143 Angle : 0.535 11.147 40927 Z= 0.279 Chirality : 0.044 0.184 4643 Planarity : 0.004 0.039 5165 Dihedral : 4.630 27.310 3994 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 17.05 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3619 helix: 0.28 (0.14), residues: 1333 sheet: -0.97 (0.22), residues: 513 loop : -0.61 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 72 TYR 0.019 0.001 TYR A 732 PHE 0.032 0.001 PHE A 938 TRP 0.012 0.001 TRP I 315 HIS 0.010 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00338 (30269) covalent geometry : angle 0.52804 (40906) hydrogen bonds : bond 0.03618 ( 1152) hydrogen bonds : angle 4.64942 ( 3303) metal coordination : bond 0.00715 ( 16) metal coordination : angle 3.73129 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 492 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6736 (pt) REVERT: A 70 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7415 (mppt) REVERT: A 140 GLN cc_start: 0.7381 (pm20) cc_final: 0.7050 (pm20) REVERT: A 182 ILE cc_start: 0.8116 (mt) cc_final: 0.7878 (mm) REVERT: A 193 ASP cc_start: 0.7418 (m-30) cc_final: 0.7034 (m-30) REVERT: A 555 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9052 (mm) REVERT: A 628 ASP cc_start: 0.7943 (t0) cc_final: 0.7586 (m-30) REVERT: A 650 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8046 (mtp180) REVERT: A 706 LEU cc_start: 0.9324 (mt) cc_final: 0.9091 (mp) REVERT: A 747 CYS cc_start: 0.8512 (t) cc_final: 0.8183 (m) REVERT: A 834 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8442 (mttp) REVERT: A 974 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8304 (ttmm) REVERT: A 1053 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6185 (tp30) REVERT: A 1200 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8217 (mmtm) REVERT: B 54 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6599 (mtm110) REVERT: B 216 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: B 297 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8340 (tppt) REVERT: B 372 ASP cc_start: 0.7656 (m-30) cc_final: 0.7342 (t70) REVERT: B 519 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: B 645 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: B 649 MET cc_start: 0.8663 (mmp) cc_final: 0.8430 (mmm) REVERT: B 652 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: B 1056 MET cc_start: 0.9132 (mtm) cc_final: 0.8920 (mtp) REVERT: B 1079 GLU cc_start: 0.7856 (pm20) cc_final: 0.7651 (mp0) REVERT: B 1082 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: B 1096 GLN cc_start: 0.7670 (mt0) cc_final: 0.7275 (mt0) REVERT: B 1102 THR cc_start: 0.8776 (p) cc_final: 0.8570 (t) REVERT: B 1131 MET cc_start: 0.9015 (mmm) cc_final: 0.8630 (mmm) REVERT: C 251 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8582 (tp) REVERT: E 21 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.8120 (ptp-170) REVERT: E 98 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (p0) REVERT: F 162 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7993 (mttp) REVERT: G 55 GLU cc_start: 0.7823 (tp30) cc_final: 0.7491 (tp30) REVERT: G 60 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7820 (mt-10) REVERT: G 104 LEU cc_start: 0.6632 (mt) cc_final: 0.6251 (mt) REVERT: I 164 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5595 (tt) REVERT: I 183 ARG cc_start: 0.5773 (mtt90) cc_final: 0.5480 (mtt90) REVERT: I 189 LEU cc_start: 0.7079 (tp) cc_final: 0.6484 (pt) REVERT: I 215 TYR cc_start: 0.7181 (t80) cc_final: 0.6865 (t80) REVERT: I 242 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7559 (ptpt) REVERT: I 261 LYS cc_start: 0.7185 (tmmt) cc_final: 0.6975 (tmmt) REVERT: I 268 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7457 (tppt) REVERT: I 294 ASP cc_start: 0.6874 (m-30) cc_final: 0.6589 (m-30) REVERT: I 659 ARG cc_start: 0.6484 (mtp85) cc_final: 0.6076 (mmt90) REVERT: I 675 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7042 (mp) REVERT: I 701 TYR cc_start: 0.6351 (m-80) cc_final: 0.5859 (m-80) REVERT: I 770 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7843 (ptmt) REVERT: S 70 SER cc_start: 0.8575 (t) cc_final: 0.8218 (m) outliers start: 101 outliers final: 39 residues processed: 538 average time/residue: 0.6754 time to fit residues: 423.8861 Evaluate side-chains 502 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 446 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1082 GLN Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 675 LEU Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 280 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 326 optimal weight: 0.0010 chunk 108 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS A 526 ASN A 611 ASN A 830 GLN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 62 GLN F 112 ASN F 140 ASN G 7 ASN I 284 HIS J 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106555 restraints weight = 37793.131| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.61 r_work: 0.3064 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30285 Z= 0.183 Angle : 0.574 12.369 40927 Z= 0.298 Chirality : 0.046 0.215 4643 Planarity : 0.004 0.043 5165 Dihedral : 4.720 26.889 3994 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.21 % Allowed : 17.62 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.48 (0.14), residues: 3619 helix: 0.37 (0.14), residues: 1339 sheet: -0.86 (0.22), residues: 489 loop : -0.59 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 720 TYR 0.020 0.001 TYR A 732 PHE 0.034 0.002 PHE A 938 TRP 0.015 0.002 TRP I 315 HIS 0.011 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00438 (30269) covalent geometry : angle 0.56697 (40906) hydrogen bonds : bond 0.03836 ( 1152) hydrogen bonds : angle 4.69709 ( 3303) metal coordination : bond 0.00883 ( 16) metal coordination : angle 3.93767 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 468 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6980 (pt) REVERT: A 140 GLN cc_start: 0.7369 (pm20) cc_final: 0.7032 (pm20) REVERT: A 182 ILE cc_start: 0.8181 (mt) cc_final: 0.7921 (mm) REVERT: A 193 ASP cc_start: 0.7454 (m-30) cc_final: 0.7075 (m-30) REVERT: A 347 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6875 (tmt170) REVERT: A 555 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9057 (mm) REVERT: A 628 ASP cc_start: 0.7926 (t0) cc_final: 0.7589 (m-30) REVERT: A 650 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: A 706 LEU cc_start: 0.9355 (mt) cc_final: 0.9127 (mp) REVERT: A 747 CYS cc_start: 0.8512 (t) cc_final: 0.8168 (m) REVERT: A 834 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: A 974 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8338 (ttmm) REVERT: A 1200 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8206 (mmtm) REVERT: B 54 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6644 (mtm110) REVERT: B 116 LYS cc_start: 0.7415 (tmtp) cc_final: 0.7159 (tptm) REVERT: B 216 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: B 297 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8351 (tppt) REVERT: B 645 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7896 (mm-40) REVERT: B 649 MET cc_start: 0.8695 (mmp) cc_final: 0.8437 (mmm) REVERT: B 1015 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8855 (t80) REVERT: B 1033 LYS cc_start: 0.8347 (mttp) cc_final: 0.7903 (mtmt) REVERT: B 1034 LYS cc_start: 0.8290 (mttm) cc_final: 0.7843 (mtmm) REVERT: B 1043 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6559 (tm-30) REVERT: B 1056 MET cc_start: 0.9144 (mtm) cc_final: 0.8893 (mtp) REVERT: B 1079 GLU cc_start: 0.7881 (pm20) cc_final: 0.7647 (mp0) REVERT: B 1096 GLN cc_start: 0.7750 (mt0) cc_final: 0.7357 (mt0) REVERT: B 1102 THR cc_start: 0.8850 (p) cc_final: 0.8561 (t) REVERT: B 1119 ASP cc_start: 0.8160 (t0) cc_final: 0.7940 (t0) REVERT: B 1131 MET cc_start: 0.9059 (mmm) cc_final: 0.8654 (mmm) REVERT: C 251 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8552 (tp) REVERT: E 21 ARG cc_start: 0.8552 (ptm-80) cc_final: 0.8120 (ptp-170) REVERT: E 98 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8225 (OUTLIER) REVERT: F 77 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8730 (tp) REVERT: F 162 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8238 (mttp) REVERT: G 55 GLU cc_start: 0.7867 (tp30) cc_final: 0.7503 (tp30) REVERT: G 60 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7831 (mt-10) REVERT: G 104 LEU cc_start: 0.6704 (mt) cc_final: 0.6316 (mt) REVERT: I 164 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5683 (tt) REVERT: I 183 ARG cc_start: 0.5753 (mtt90) cc_final: 0.5353 (mtp-110) REVERT: I 189 LEU cc_start: 0.7123 (tp) cc_final: 0.6528 (pt) REVERT: I 215 TYR cc_start: 0.7193 (t80) cc_final: 0.6859 (t80) REVERT: I 242 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7615 (ptpt) REVERT: I 268 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7468 (tppt) REVERT: I 294 ASP cc_start: 0.6850 (m-30) cc_final: 0.6580 (m-30) REVERT: I 659 ARG cc_start: 0.6552 (mtp85) cc_final: 0.6128 (mmt90) REVERT: I 667 LYS cc_start: 0.7049 (mtmm) cc_final: 0.6759 (ptpp) REVERT: I 701 TYR cc_start: 0.6353 (m-80) cc_final: 0.5768 (m-80) REVERT: I 715 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8084 (tmt) REVERT: I 770 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7883 (ptmt) REVERT: S 70 SER cc_start: 0.8578 (t) cc_final: 0.8222 (m) REVERT: S 149 ASN cc_start: 0.6243 (p0) cc_final: 0.5702 (m-40) outliers start: 108 outliers final: 50 residues processed: 520 average time/residue: 0.6488 time to fit residues: 393.7564 Evaluate side-chains 508 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 442 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 242 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 268 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 357 optimal weight: 0.0270 chunk 228 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 173 optimal weight: 0.9980 overall best weight: 0.7856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN F 112 ASN F 140 ASN G 7 ASN I 284 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109126 restraints weight = 37542.158| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.61 r_work: 0.3109 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30285 Z= 0.115 Angle : 0.531 10.506 40927 Z= 0.276 Chirality : 0.044 0.179 4643 Planarity : 0.003 0.052 5165 Dihedral : 4.503 26.148 3994 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.71 % Allowed : 18.48 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.26 (0.14), residues: 3619 helix: 0.63 (0.14), residues: 1339 sheet: -0.78 (0.22), residues: 496 loop : -0.52 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 72 TYR 0.016 0.001 TYR A 732 PHE 0.030 0.001 PHE A 938 TRP 0.013 0.001 TRP I 315 HIS 0.009 0.001 HIS I 284 Details of bonding type rmsd covalent geometry : bond 0.00269 (30269) covalent geometry : angle 0.52570 (40906) hydrogen bonds : bond 0.03424 ( 1152) hydrogen bonds : angle 4.55233 ( 3303) metal coordination : bond 0.00476 ( 16) metal coordination : angle 3.34311 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 471 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6788 (pt) REVERT: A 70 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7558 (mppt) REVERT: A 140 GLN cc_start: 0.7304 (pm20) cc_final: 0.7070 (pm20) REVERT: A 182 ILE cc_start: 0.8117 (mt) cc_final: 0.7849 (mm) REVERT: A 193 ASP cc_start: 0.7417 (m-30) cc_final: 0.6992 (m-30) REVERT: A 555 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9052 (mm) REVERT: A 628 ASP cc_start: 0.7897 (t0) cc_final: 0.7564 (m-30) REVERT: A 747 CYS cc_start: 0.8441 (t) cc_final: 0.8159 (m) REVERT: A 834 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8427 (mttp) REVERT: A 862 ASP cc_start: 0.7878 (m-30) cc_final: 0.7566 (m-30) REVERT: A 974 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8268 (ttmm) REVERT: A 1161 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: A 1200 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8217 (mmtm) REVERT: B 54 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6534 (mtm110) REVERT: B 216 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: B 297 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8355 (tppt) REVERT: B 372 ASP cc_start: 0.7603 (m-30) cc_final: 0.7331 (t70) REVERT: B 427 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8032 (pmm-80) REVERT: B 645 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7884 (mm-40) REVERT: B 649 MET cc_start: 0.8701 (mmp) cc_final: 0.8443 (mmm) REVERT: B 652 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8180 (mttp) REVERT: B 1033 LYS cc_start: 0.8316 (mttp) cc_final: 0.7889 (mtmt) REVERT: B 1034 LYS cc_start: 0.8235 (mttm) cc_final: 0.7782 (mtmm) REVERT: B 1096 GLN cc_start: 0.7649 (mt0) cc_final: 0.7272 (mt0) REVERT: B 1102 THR cc_start: 0.8762 (p) cc_final: 0.8546 (t) REVERT: B 1131 MET cc_start: 0.9018 (mmm) cc_final: 0.8594 (mmm) REVERT: B 1145 ARG cc_start: 0.6856 (mtm110) cc_final: 0.6278 (mtm180) REVERT: C 251 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8541 (tp) REVERT: E 21 ARG cc_start: 0.8483 (ptm-80) cc_final: 0.8087 (ptp-170) REVERT: E 98 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8212 (OUTLIER) REVERT: F 77 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8705 (tp) REVERT: F 162 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8220 (mttp) REVERT: G 55 GLU cc_start: 0.7825 (tp30) cc_final: 0.7126 (tp30) REVERT: G 60 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 104 LEU cc_start: 0.6606 (mt) cc_final: 0.6229 (mt) REVERT: I 121 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5736 (mpt) REVERT: I 164 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5621 (tt) REVERT: I 183 ARG cc_start: 0.5722 (mtt90) cc_final: 0.5462 (mtt90) REVERT: I 189 LEU cc_start: 0.7135 (tp) cc_final: 0.6523 (pt) REVERT: I 215 TYR cc_start: 0.7094 (t80) cc_final: 0.6750 (t80) REVERT: I 242 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (ptpt) REVERT: I 268 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7463 (tppt) REVERT: I 294 ASP cc_start: 0.6839 (m-30) cc_final: 0.6587 (m-30) REVERT: I 659 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6113 (mmt90) REVERT: S 70 SER cc_start: 0.8622 (t) cc_final: 0.8268 (m) outliers start: 91 outliers final: 34 residues processed: 518 average time/residue: 0.6819 time to fit residues: 410.3499 Evaluate side-chains 484 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 434 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 242 LYS Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 741 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 147 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 994 ASN B 481 GLN B 958 ASN B1023 GLN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 112 ASN F 140 ASN G 7 ASN I 284 HIS I 795 ASN J 53 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108799 restraints weight = 37658.732| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.62 r_work: 0.3098 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30285 Z= 0.133 Angle : 0.547 10.514 40927 Z= 0.282 Chirality : 0.044 0.181 4643 Planarity : 0.004 0.046 5165 Dihedral : 4.479 27.175 3994 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.41 % Allowed : 19.40 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.15 (0.14), residues: 3619 helix: 0.74 (0.14), residues: 1339 sheet: -0.71 (0.22), residues: 494 loop : -0.48 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 72 TYR 0.025 0.001 TYR I 701 PHE 0.031 0.001 PHE A 938 TRP 0.014 0.001 TRP I 315 HIS 0.009 0.001 HIS I 284 Details of bonding type rmsd covalent geometry : bond 0.00316 (30269) covalent geometry : angle 0.54204 (40906) hydrogen bonds : bond 0.03465 ( 1152) hydrogen bonds : angle 4.51367 ( 3303) metal coordination : bond 0.00561 ( 16) metal coordination : angle 3.36451 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 439 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6714 (pt) REVERT: A 140 GLN cc_start: 0.7319 (pm20) cc_final: 0.6989 (pm20) REVERT: A 182 ILE cc_start: 0.8147 (mt) cc_final: 0.7875 (mm) REVERT: A 193 ASP cc_start: 0.7467 (m-30) cc_final: 0.7021 (m-30) REVERT: A 555 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9073 (mm) REVERT: A 628 ASP cc_start: 0.7879 (t0) cc_final: 0.7583 (m-30) REVERT: A 650 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8017 (mtp180) REVERT: A 706 LEU cc_start: 0.9318 (mp) cc_final: 0.9113 (mt) REVERT: A 747 CYS cc_start: 0.8374 (t) cc_final: 0.8107 (m) REVERT: A 834 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: A 862 ASP cc_start: 0.7840 (m-30) cc_final: 0.7510 (m-30) REVERT: A 974 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8277 (ttmm) REVERT: A 1161 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: B 54 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6542 (mtm110) REVERT: B 116 LYS cc_start: 0.7342 (tmtp) cc_final: 0.7123 (tptm) REVERT: B 216 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: B 273 ARG cc_start: 0.7402 (ttp80) cc_final: 0.7164 (ttp80) REVERT: B 297 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8353 (tppt) REVERT: B 372 ASP cc_start: 0.7600 (m-30) cc_final: 0.7316 (t0) REVERT: B 427 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8036 (pmm-80) REVERT: B 554 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8090 (ttp80) REVERT: B 645 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7889 (mm-40) REVERT: B 649 MET cc_start: 0.8719 (mmp) cc_final: 0.8451 (mmm) REVERT: B 652 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8135 (mttp) REVERT: B 1033 LYS cc_start: 0.8344 (mttp) cc_final: 0.7926 (mtmt) REVERT: B 1034 LYS cc_start: 0.8225 (mttm) cc_final: 0.7808 (mtmm) REVERT: B 1096 GLN cc_start: 0.7708 (mt0) cc_final: 0.7326 (mt0) REVERT: B 1131 MET cc_start: 0.9029 (mmm) cc_final: 0.8692 (mmm) REVERT: B 1145 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6311 (mtm180) REVERT: C 251 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8546 (tp) REVERT: E 21 ARG cc_start: 0.8487 (ptm-80) cc_final: 0.8088 (ptp-170) REVERT: E 29 ARG cc_start: 0.8731 (ptt-90) cc_final: 0.8489 (ptm160) REVERT: E 98 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8186 (p0) REVERT: F 77 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8710 (tp) REVERT: F 162 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7982 (mttp) REVERT: G 55 GLU cc_start: 0.7793 (tp30) cc_final: 0.7452 (tp30) REVERT: G 60 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7866 (mt-10) REVERT: I 164 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5596 (tt) REVERT: I 168 MET cc_start: 0.6734 (ptp) cc_final: 0.6514 (ptp) REVERT: I 169 LYS cc_start: 0.6350 (mmtt) cc_final: 0.6095 (mmmt) REVERT: I 183 ARG cc_start: 0.5783 (mtt90) cc_final: 0.5330 (mtp-110) REVERT: I 189 LEU cc_start: 0.7154 (tp) cc_final: 0.6529 (pt) REVERT: I 215 TYR cc_start: 0.7128 (t80) cc_final: 0.6693 (t80) REVERT: I 242 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7633 (ptpt) REVERT: I 268 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7414 (tppt) REVERT: I 659 ARG cc_start: 0.6521 (mtp85) cc_final: 0.6088 (mmt90) REVERT: S 50 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8026 (ttmm) REVERT: S 70 SER cc_start: 0.8596 (t) cc_final: 0.8246 (m) outliers start: 81 outliers final: 41 residues processed: 482 average time/residue: 0.6898 time to fit residues: 386.2874 Evaluate side-chains 476 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 418 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 242 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 297 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 360 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN B 481 GLN B 977 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN F 112 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107721 restraints weight = 37571.387| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.81 r_work: 0.3071 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30285 Z= 0.157 Angle : 0.568 12.494 40927 Z= 0.293 Chirality : 0.045 0.188 4643 Planarity : 0.004 0.049 5165 Dihedral : 4.541 28.667 3994 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.41 % Allowed : 19.61 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.14 (0.14), residues: 3619 helix: 0.74 (0.14), residues: 1339 sheet: -0.68 (0.22), residues: 495 loop : -0.47 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 72 TYR 0.021 0.001 TYR I 701 PHE 0.033 0.001 PHE A 938 TRP 0.018 0.001 TRP I 315 HIS 0.009 0.001 HIS I 284 Details of bonding type rmsd covalent geometry : bond 0.00377 (30269) covalent geometry : angle 0.56243 (40906) hydrogen bonds : bond 0.03598 ( 1152) hydrogen bonds : angle 4.54879 ( 3303) metal coordination : bond 0.00713 ( 16) metal coordination : angle 3.61051 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 434 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6745 (pt) REVERT: A 182 ILE cc_start: 0.8149 (mt) cc_final: 0.7874 (mm) REVERT: A 193 ASP cc_start: 0.7496 (m-30) cc_final: 0.7045 (m-30) REVERT: A 555 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9079 (mm) REVERT: A 628 ASP cc_start: 0.7936 (t0) cc_final: 0.7598 (m-30) REVERT: A 650 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8039 (mtp180) REVERT: A 747 CYS cc_start: 0.8420 (t) cc_final: 0.8123 (m) REVERT: A 834 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8459 (mttp) REVERT: A 862 ASP cc_start: 0.7868 (m-30) cc_final: 0.7559 (m-30) REVERT: A 974 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8292 (ttmm) REVERT: A 1056 MET cc_start: 0.8424 (ttt) cc_final: 0.8222 (ttt) REVERT: A 1161 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: A 1200 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8241 (mmtm) REVERT: B 54 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6557 (mtm110) REVERT: B 116 LYS cc_start: 0.7315 (tmtp) cc_final: 0.7069 (tptm) REVERT: B 216 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: B 297 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8361 (tppt) REVERT: B 427 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8023 (pmm-80) REVERT: B 554 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (ttp80) REVERT: B 645 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7916 (mm-40) REVERT: B 649 MET cc_start: 0.8748 (mmp) cc_final: 0.8480 (mmm) REVERT: B 652 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8189 (mttp) REVERT: B 1033 LYS cc_start: 0.8359 (mttp) cc_final: 0.7901 (mtmt) REVERT: B 1034 LYS cc_start: 0.8269 (mttm) cc_final: 0.7774 (mtmm) REVERT: B 1096 GLN cc_start: 0.7760 (mt0) cc_final: 0.7361 (mt0) REVERT: B 1131 MET cc_start: 0.9063 (mmm) cc_final: 0.8745 (mmm) REVERT: B 1145 ARG cc_start: 0.6953 (mtm110) cc_final: 0.6376 (mtm180) REVERT: C 251 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8545 (tp) REVERT: E 21 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8115 (ptp-170) REVERT: E 98 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (p0) REVERT: F 77 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8719 (tp) REVERT: F 162 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: G 55 GLU cc_start: 0.7796 (tp30) cc_final: 0.7414 (tp30) REVERT: G 60 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7924 (mt-10) REVERT: I 121 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5811 (mpt) REVERT: I 164 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5697 (tt) REVERT: I 168 MET cc_start: 0.6751 (ptp) cc_final: 0.6523 (ptp) REVERT: I 169 LYS cc_start: 0.6374 (mmtt) cc_final: 0.6120 (mmmt) REVERT: I 183 ARG cc_start: 0.5752 (mtt90) cc_final: 0.5546 (mtt180) REVERT: I 186 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7281 (mmtm) REVERT: I 189 LEU cc_start: 0.7220 (tp) cc_final: 0.6573 (pt) REVERT: I 215 TYR cc_start: 0.7124 (t80) cc_final: 0.6758 (t80) REVERT: I 242 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7639 (ptpt) REVERT: I 268 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7455 (tppt) REVERT: I 659 ARG cc_start: 0.6558 (mtp85) cc_final: 0.6129 (mmt90) REVERT: I 715 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8041 (tmt) REVERT: S 50 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8035 (ttmm) outliers start: 81 outliers final: 43 residues processed: 476 average time/residue: 0.6996 time to fit residues: 387.6390 Evaluate side-chains 489 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 426 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1200 LYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain B residue 1114 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 242 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 715 MET Chi-restraints excluded: chain I residue 776 GLN Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 138 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 227 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 303 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 276 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN B 481 GLN B1089 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110007 restraints weight = 37572.919| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.73 r_work: 0.3105 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30285 Z= 0.118 Angle : 0.552 12.249 40927 Z= 0.283 Chirality : 0.044 0.178 4643 Planarity : 0.004 0.058 5165 Dihedral : 4.420 26.111 3994 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 20.15 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.01 (0.14), residues: 3619 helix: 0.90 (0.15), residues: 1332 sheet: -0.65 (0.22), residues: 502 loop : -0.42 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 72 TYR 0.022 0.001 TYR I 109 PHE 0.029 0.001 PHE A 938 TRP 0.017 0.001 TRP I 315 HIS 0.010 0.001 HIS I 284 Details of bonding type rmsd covalent geometry : bond 0.00278 (30269) covalent geometry : angle 0.54738 (40906) hydrogen bonds : bond 0.03355 ( 1152) hydrogen bonds : angle 4.46705 ( 3303) metal coordination : bond 0.00447 ( 16) metal coordination : angle 3.17777 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 451 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6739 (pt) REVERT: A 182 ILE cc_start: 0.8134 (mt) cc_final: 0.7863 (mm) REVERT: A 193 ASP cc_start: 0.7454 (m-30) cc_final: 0.6998 (m-30) REVERT: A 555 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 650 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8028 (mtp180) REVERT: A 706 LEU cc_start: 0.9304 (mp) cc_final: 0.9095 (mt) REVERT: A 747 CYS cc_start: 0.8322 (t) cc_final: 0.8089 (m) REVERT: A 834 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: A 862 ASP cc_start: 0.7807 (m-30) cc_final: 0.7518 (m-30) REVERT: A 974 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8279 (ttmm) REVERT: A 1161 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: B 116 LYS cc_start: 0.7372 (tmtp) cc_final: 0.7145 (tptm) REVERT: B 216 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 288 ASN cc_start: 0.7472 (m-40) cc_final: 0.7028 (m-40) REVERT: B 297 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8369 (tppt) REVERT: B 372 ASP cc_start: 0.7610 (m-30) cc_final: 0.7191 (t0) REVERT: B 427 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8013 (pmm-80) REVERT: B 645 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7905 (mm-40) REVERT: B 649 MET cc_start: 0.8721 (mmp) cc_final: 0.8456 (mmm) REVERT: B 652 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8154 (mttp) REVERT: B 1033 LYS cc_start: 0.8349 (mttp) cc_final: 0.7895 (mtmt) REVERT: B 1034 LYS cc_start: 0.8200 (mttm) cc_final: 0.7743 (mtmm) REVERT: B 1096 GLN cc_start: 0.7736 (mt0) cc_final: 0.7329 (mt0) REVERT: B 1119 ASP cc_start: 0.8183 (t0) cc_final: 0.7976 (t0) REVERT: B 1131 MET cc_start: 0.9029 (mmm) cc_final: 0.8666 (mmm) REVERT: B 1145 ARG cc_start: 0.6883 (mtm110) cc_final: 0.6267 (mtm180) REVERT: C 251 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8554 (tp) REVERT: C 285 GLU cc_start: 0.7337 (pm20) cc_final: 0.6950 (pm20) REVERT: E 21 ARG cc_start: 0.8508 (ptm-80) cc_final: 0.8094 (ptp-170) REVERT: E 62 GLN cc_start: 0.8788 (mt0) cc_final: 0.8520 (mt0) REVERT: E 98 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8232 (OUTLIER) REVERT: F 77 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8695 (tp) REVERT: F 162 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7960 (mttp) REVERT: G 55 GLU cc_start: 0.7793 (tp30) cc_final: 0.7414 (tp30) REVERT: G 60 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7890 (mt-10) REVERT: G 104 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6233 (mt) REVERT: G 142 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6430 (mtt) REVERT: I 164 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5624 (tt) REVERT: I 169 LYS cc_start: 0.6342 (mmtt) cc_final: 0.6096 (mmmt) REVERT: I 186 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7256 (mmtm) REVERT: I 189 LEU cc_start: 0.7205 (tp) cc_final: 0.6560 (pt) REVERT: I 215 TYR cc_start: 0.7111 (t80) cc_final: 0.6737 (t80) REVERT: I 242 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7648 (ptpt) REVERT: I 268 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7471 (tppt) REVERT: I 659 ARG cc_start: 0.6607 (mtp85) cc_final: 0.6183 (mmt90) REVERT: S 50 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8060 (ttmm) outliers start: 63 outliers final: 37 residues processed: 483 average time/residue: 0.6857 time to fit residues: 385.7018 Evaluate side-chains 483 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 430 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 834 LYS Chi-restraints excluded: chain A residue 859 ASP Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 976 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 101 CYS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain I residue 242 LYS Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain S residue 115 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 43 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 243 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 GLN B 977 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 HIS S 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109948 restraints weight = 37601.765| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.62 r_work: 0.3122 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30285 Z= 0.122 Angle : 0.555 12.290 40927 Z= 0.284 Chirality : 0.044 0.202 4643 Planarity : 0.004 0.056 5165 Dihedral : 4.380 26.665 3994 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.82 % Allowed : 20.51 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.06 (0.14), residues: 3619 helix: 0.96 (0.15), residues: 1327 sheet: -0.60 (0.22), residues: 493 loop : -0.39 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 273 TYR 0.022 0.001 TYR A 222 PHE 0.029 0.001 PHE A 938 TRP 0.014 0.001 TRP I 315 HIS 0.010 0.001 HIS I 284 Details of bonding type rmsd covalent geometry : bond 0.00288 (30269) covalent geometry : angle 0.55071 (40906) hydrogen bonds : bond 0.03366 ( 1152) hydrogen bonds : angle 4.44012 ( 3303) metal coordination : bond 0.00476 ( 16) metal coordination : angle 3.15481 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12239.18 seconds wall clock time: 208 minutes 45.82 seconds (12525.82 seconds total)