Starting phenix.real_space_refine on Thu Jun 19 22:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.map" model { file = "/net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usd_26733/06_2025/7usd_26733.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.007 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 P 3 5.49 5 Mg 1 5.21 5 S 155 5.16 5 C 14794 2.51 5 N 3960 2.21 5 O 4313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23226 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9709 Classifications: {'peptide': 1185} Link IDs: {'PTRANS': 45, 'TRANS': 1139} Chain breaks: 6 Chain: "B" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8773 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 38, 'TRANS': 1055} Chain breaks: 3 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1576 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 8, 'TRANS': 182} Chain breaks: 2 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1379 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.76, per 1000 atoms: 0.59 Number of scatterers: 23226 At special positions: 0 Unit cell: (141.863, 141.863, 207.541, 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) S 155 16.00 P 3 15.00 Mg 1 11.99 O 4313 8.00 N 3960 7.00 C 14794 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: 6.49 Conformation dependent library (CDL) restraints added in 3.1 seconds 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 8 sheets defined 76.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 58 through 85 removed outlier: 3.914A pdb=" N GLN A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 144 removed outlier: 3.986A pdb=" N TYR A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.724A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.362A pdb=" N LYS A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 removed outlier: 3.649A pdb=" N LEU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.880A pdb=" N ASN A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.015A pdb=" N VAL A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.778A pdb=" N LEU A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 removed outlier: 3.628A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 302 removed outlier: 4.152A pdb=" N ILE A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 325 through 332 removed outlier: 4.121A pdb=" N LYS A 329 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 330 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 365 removed outlier: 4.061A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.567A pdb=" N TYR A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.648A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 491 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'A' and resid 504 through 518 removed outlier: 3.541A pdb=" N VAL A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 4.041A pdb=" N ARG A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 585 through 599 removed outlier: 3.597A pdb=" N ILE A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 617 through 622 removed outlier: 5.607A pdb=" N GLN A 620 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP A 622 " --> pdb=" O SER A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 624 through 630 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 658 through 664 removed outlier: 4.246A pdb=" N GLU A 662 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 684 through 723 removed outlier: 3.713A pdb=" N TYR A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 745 through 751 removed outlier: 4.379A pdb=" N LEU A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 789 removed outlier: 3.512A pdb=" N LEU A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 793 No H-bonds generated for 'chain 'A' and resid 791 through 793' Processing helix chain 'A' and resid 794 through 813 Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 837 through 850 Processing helix chain 'A' and resid 891 through 903 Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 910 through 922 Processing helix chain 'A' and resid 923 through 942 Processing helix chain 'A' and resid 943 through 956 removed outlier: 3.549A pdb=" N GLU A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 955 " --> pdb=" O THR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 980 Processing helix chain 'A' and resid 980 through 986 Processing helix chain 'A' and resid 992 through 1026 Processing helix chain 'A' and resid 1027 through 1030 removed outlier: 3.902A pdb=" N ASN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1030' Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1055 through 1058 Processing helix chain 'A' and resid 1059 through 1066 Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1085 through 1088 Processing helix chain 'A' and resid 1092 through 1104 removed outlier: 3.760A pdb=" N ILE A1096 " --> pdb=" O MET A1092 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 3.733A pdb=" N LEU A1130 " --> pdb=" O GLU A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 3.568A pdb=" N CYS A1152 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1168 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1200 through 1227 removed outlier: 3.543A pdb=" N MET A1204 " --> pdb=" O PRO A1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 4.125A pdb=" N LYS B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 12' Processing helix chain 'B' and resid 12 through 40 removed outlier: 3.848A pdb=" N ASP B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.674A pdb=" N LYS B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 90 through 118 Processing helix chain 'B' and resid 126 through 150 Processing helix chain 'B' and resid 152 through 169 removed outlier: 3.662A pdb=" N ILE B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.979A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 removed outlier: 3.692A pdb=" N SER B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.688A pdb=" N SER B 234 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.717A pdb=" N GLU B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 269 through 276 removed outlier: 4.123A pdb=" N LEU B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 303 through 313 removed outlier: 4.439A pdb=" N ASN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 360 removed outlier: 5.764A pdb=" N GLY B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.763A pdb=" N GLY B 365 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.825A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 removed outlier: 3.585A pdb=" N LEU B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 437 removed outlier: 3.783A pdb=" N MET B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.585A pdb=" N GLN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 470 Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.991A pdb=" N GLU B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 477' Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'B' and resid 505 through 508 removed outlier: 3.770A pdb=" N ASP B 508 " --> pdb=" O GLY B 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 509 through 528 Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.517A pdb=" N PHE B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 561 through 566 removed outlier: 3.812A pdb=" N ARG B 564 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.677A pdb=" N THR B 574 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.559A pdb=" N CYS B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 627 removed outlier: 4.344A pdb=" N HIS B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 removed outlier: 6.079A pdb=" N LYS B 631 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 673 through 690 removed outlier: 3.850A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 723 removed outlier: 3.846A pdb=" N TYR B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 753 removed outlier: 3.554A pdb=" N SER B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 761 through 774 removed outlier: 3.568A pdb=" N GLN B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 796 Processing helix chain 'B' and resid 796 through 802 removed outlier: 3.507A pdb=" N SER B 801 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 802 " --> pdb=" O ARG B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 832 through 844 Processing helix chain 'B' and resid 844 through 873 removed outlier: 3.574A pdb=" N LYS B 868 " --> pdb=" O ALA B 864 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 883 removed outlier: 4.052A pdb=" N THR B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 897 removed outlier: 3.874A pdb=" N ALA B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 932 removed outlier: 4.125A pdb=" N VAL B 903 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 904 " --> pdb=" O VAL B 900 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR B 930 " --> pdb=" O ASP B 926 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 931 " --> pdb=" O VAL B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 945 Processing helix chain 'B' and resid 951 through 965 removed outlier: 3.893A pdb=" N ASN B 957 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 965 " --> pdb=" O LEU B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 981 Processing helix chain 'B' and resid 988 through 1007 removed outlier: 3.673A pdb=" N MET B1000 " --> pdb=" O ALA B 996 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B1001 " --> pdb=" O CYS B 997 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B1006 " --> pdb=" O PHE B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1017 removed outlier: 3.523A pdb=" N SER B1012 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL B1014 " --> pdb=" O ALA B1011 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N MET B1015 " --> pdb=" O SER B1012 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B1017 " --> pdb=" O VAL B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1030 No H-bonds generated for 'chain 'B' and resid 1028 through 1030' Processing helix chain 'B' and resid 1031 through 1047 Processing helix chain 'B' and resid 1050 through 1072 removed outlier: 3.785A pdb=" N GLN B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B1072 " --> pdb=" O LYS B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.660A pdb=" N LEU B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B1088 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B1089 " --> pdb=" O TYR B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 removed outlier: 3.516A pdb=" N LEU B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1119 removed outlier: 4.168A pdb=" N LEU B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 81 removed outlier: 4.009A pdb=" N ILE C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 removed outlier: 4.193A pdb=" N MET C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.503A pdb=" N VAL C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.692A pdb=" N THR C 138 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Proline residue: C 139 - end of helix Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 155 through 177 removed outlier: 3.696A pdb=" N LYS C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 515 Processing helix chain 'C' and resid 530 through 542 Processing helix chain 'D' and resid 11 through 68 removed outlier: 3.570A pdb=" N SER D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 11 through 39 removed outlier: 3.686A pdb=" N ILE E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 110 removed outlier: 3.507A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.827A pdb=" N ASP F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 86 through 105 removed outlier: 4.157A pdb=" N ARG F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Proline residue: F 99 - end of helix Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.948A pdb=" N LYS F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 165 through 178 removed outlier: 4.158A pdb=" N PHE F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 308 removed outlier: 7.175A pdb=" N MET A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 755 through 757 removed outlier: 3.649A pdb=" N VAL A 755 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 855 through 858 removed outlier: 3.524A pdb=" N VAL A 865 " --> pdb=" O CYS A 856 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1090 through 1091 Processing sheet with id=AA5, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'B' and resid 695 through 697 Processing sheet with id=AA7, first strand: chain 'B' and resid 805 through 808 Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 46 removed outlier: 4.026A pdb=" N ASP F 38 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE F 4 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TRP F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS F 6 " --> pdb=" O TRP F 56 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR F 58 " --> pdb=" O CYS F 6 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL F 8 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL F 77 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE F 78 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 113 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE F 80 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE F 82 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE F 110 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N LEU F 155 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU F 112 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 1502 hydrogen bonds defined for protein. 4359 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: 9.34 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4037 1.32 - 1.45: 5953 1.45 - 1.57: 13434 1.57 - 1.69: 5 1.69 - 1.81: 249 Bond restraints: 23678 Sorted by residual: bond pdb=" C ALA F 172 " pdb=" O ALA F 172 " ideal model delta sigma weight residual 1.237 1.298 -0.061 1.17e-02 7.31e+03 2.74e+01 bond pdb=" N MET B 392 " pdb=" CA MET B 392 " ideal model delta sigma weight residual 1.458 1.490 -0.033 7.40e-03 1.83e+04 1.96e+01 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.246 1.208 0.037 8.50e-03 1.38e+04 1.92e+01 bond pdb=" C GLU E 27 " pdb=" O GLU E 27 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" C PHE E 20 " pdb=" O PHE E 20 " ideal model delta sigma weight residual 1.237 1.283 -0.047 1.19e-02 7.06e+03 1.54e+01 ... (remaining 23673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 31329 2.38 - 4.77: 625 4.77 - 7.15: 31 7.15 - 9.53: 6 9.53 - 11.92: 3 Bond angle restraints: 31994 Sorted by residual: angle pdb=" C ALA B 235 " pdb=" N PRO B 236 " pdb=" CA PRO B 236 " ideal model delta sigma weight residual 119.28 126.42 -7.14 1.10e+00 8.26e-01 4.21e+01 angle pdb=" N ALA A1025 " pdb=" CA ALA A1025 " pdb=" C ALA A1025 " ideal model delta sigma weight residual 113.20 119.60 -6.40 1.21e+00 6.83e-01 2.80e+01 angle pdb=" N MET C 97 " pdb=" CA MET C 97 " pdb=" C MET C 97 " ideal model delta sigma weight residual 113.01 107.44 5.57 1.20e+00 6.94e-01 2.15e+01 angle pdb=" N ASP E 21 " pdb=" CA ASP E 21 " pdb=" C ASP E 21 " ideal model delta sigma weight residual 111.28 106.42 4.86 1.09e+00 8.42e-01 1.99e+01 angle pdb=" CA VAL A 868 " pdb=" C VAL A 868 " pdb=" O VAL A 868 " ideal model delta sigma weight residual 120.95 116.49 4.46 1.04e+00 9.25e-01 1.84e+01 ... (remaining 31989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 14115 32.44 - 64.89: 334 64.89 - 97.33: 38 97.33 - 129.77: 3 129.77 - 162.22: 2 Dihedral angle restraints: 14492 sinusoidal: 5995 harmonic: 8497 Sorted by residual: dihedral pdb=" C8 GTP F 201 " pdb=" C1' GTP F 201 " pdb=" N9 GTP F 201 " pdb=" O4' GTP F 201 " ideal model delta sinusoidal sigma weight residual 104.59 -57.63 162.22 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O5' GTP F 201 " pdb=" O3A GTP F 201 " pdb=" PA GTP F 201 " pdb=" PB GTP F 201 " ideal model delta sinusoidal sigma weight residual 274.12 142.74 131.39 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' GTP F 201 " pdb=" O5' GTP F 201 " pdb=" PA GTP F 201 " pdb=" O3A GTP F 201 " ideal model delta sinusoidal sigma weight residual 69.27 -54.88 124.15 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 14489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3257 0.073 - 0.147: 306 0.147 - 0.220: 39 0.220 - 0.293: 10 0.293 - 0.367: 3 Chirality restraints: 3615 Sorted by residual: chirality pdb=" CA THR E 54 " pdb=" N THR E 54 " pdb=" C THR E 54 " pdb=" CB THR E 54 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA LYS E 116 " pdb=" N LYS E 116 " pdb=" C LYS E 116 " pdb=" CB LYS E 116 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CG LEU D 47 " pdb=" CB LEU D 47 " pdb=" CD1 LEU D 47 " pdb=" CD2 LEU D 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3612 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 170 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ASP F 170 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP F 170 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU F 171 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 126 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP C 126 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP C 126 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL C 127 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B1051 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C ILE B1051 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE B1051 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU B1052 " -0.016 2.00e-02 2.50e+03 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2506 2.75 - 3.28: 24229 3.28 - 3.82: 38914 3.82 - 4.36: 44610 4.36 - 4.90: 78840 Nonbonded interactions: 189099 Sorted by model distance: nonbonded pdb=" NE ARG A 760 " pdb=" OG1 THR C 116 " model vdw 2.207 3.120 nonbonded pdb=" O ALA F 59 " pdb=" NH1 ARG F 68 " model vdw 2.207 3.120 nonbonded pdb=" O VAL A 992 " pdb=" OD1 ASN A 996 " model vdw 2.233 3.040 nonbonded pdb=" N GLU A 61 " pdb=" OE1 GLU A 61 " model vdw 2.234 3.120 nonbonded pdb=" O SER E 40 " pdb=" NZ LYS E 43 " model vdw 2.244 3.120 ... (remaining 189094 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: 1.320 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 55.640 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.004 0.061 23678 Z= 0.305 Angle : 0.703 11.916 31994 Z= 0.476 Chirality : 0.046 0.367 3615 Planarity : 0.004 0.051 4073 Dihedral : 14.520 162.218 8958 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.15 % Allowed : 1.04 % Favored : 98.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.17), residues: 2830 helix: 3.08 (0.12), residues: 1927 sheet: -0.63 (0.60), residues: 69 loop : 0.43 (0.24), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 845 HIS 0.006 0.001 HIS C 60 PHE 0.013 0.001 PHE C 64 TYR 0.023 0.001 TYR A1138 ARG 0.013 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.14256 ( 1502) hydrogen bonds : angle 4.45441 ( 4359) covalent geometry : bond 0.00424 (23678) covalent geometry : angle 0.70311 (31994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 550 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8080 (m-30) cc_final: 0.7848 (m-30) REVERT: A 135 ARG cc_start: 0.7239 (tpp80) cc_final: 0.6623 (ttt-90) REVERT: A 208 GLN cc_start: 0.7704 (tp40) cc_final: 0.7471 (tp40) REVERT: A 279 SER cc_start: 0.8124 (t) cc_final: 0.7806 (p) REVERT: A 333 THR cc_start: 0.8738 (p) cc_final: 0.8489 (t) REVERT: A 422 LYS cc_start: 0.8566 (pttp) cc_final: 0.8316 (pttp) REVERT: A 546 LYS cc_start: 0.7677 (tptt) cc_final: 0.7288 (pttp) REVERT: A 594 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7152 (ttmm) REVERT: A 726 ARG cc_start: 0.7405 (tpp80) cc_final: 0.7133 (tpp80) REVERT: A 988 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 1216 ASP cc_start: 0.7263 (m-30) cc_final: 0.6994 (m-30) REVERT: B 411 TYR cc_start: 0.7504 (m-80) cc_final: 0.7123 (m-80) REVERT: B 458 ILE cc_start: 0.8080 (mm) cc_final: 0.7866 (mm) REVERT: B 462 SER cc_start: 0.8418 (t) cc_final: 0.8068 (p) REVERT: B 552 MET cc_start: 0.8185 (mtt) cc_final: 0.7973 (mtm) REVERT: B 725 MET cc_start: 0.7844 (mmt) cc_final: 0.7444 (mmm) REVERT: B 940 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 1057 GLU cc_start: 0.7303 (tt0) cc_final: 0.6916 (mm-30) REVERT: C 78 VAL cc_start: 0.7072 (p) cc_final: 0.6729 (m) REVERT: C 106 ILE cc_start: 0.8151 (mm) cc_final: 0.7928 (pp) REVERT: C 108 ASP cc_start: 0.8999 (m-30) cc_final: 0.8798 (m-30) REVERT: C 119 ILE cc_start: 0.8169 (mm) cc_final: 0.7464 (mm) REVERT: C 164 LYS cc_start: 0.8018 (tmmt) cc_final: 0.7685 (tmmm) REVERT: C 167 GLN cc_start: 0.6762 (tp40) cc_final: 0.6299 (pp30) REVERT: D 61 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7270 (tp) REVERT: E 49 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7134 (mp0) REVERT: F 35 THR cc_start: 0.7765 (p) cc_final: 0.7559 (p) REVERT: F 90 PHE cc_start: 0.7478 (t80) cc_final: 0.6770 (t80) REVERT: F 91 GLU cc_start: 0.8799 (tp30) cc_final: 0.8413 (tp30) REVERT: F 122 ASP cc_start: 0.8056 (t0) cc_final: 0.7632 (t0) outliers start: 4 outliers final: 5 residues processed: 554 average time/residue: 1.5894 time to fit residues: 991.7891 Evaluate side-chains 359 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 353 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.0970 chunk 215 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 505 ASN B 33 ASN B 199 HIS B 218 ASN B 274 ASN D 51 ASN E 70 ASN E 71 ASN E 74 GLN F 162 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099825 restraints weight = 35608.225| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.62 r_work: 0.3249 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23678 Z= 0.127 Angle : 0.526 7.370 31994 Z= 0.274 Chirality : 0.038 0.168 3615 Planarity : 0.004 0.041 4073 Dihedral : 6.566 158.875 3155 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.04 % Allowed : 10.96 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.16), residues: 2830 helix: 2.87 (0.12), residues: 1932 sheet: -0.74 (0.53), residues: 77 loop : 0.33 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 698 HIS 0.006 0.001 HIS A 754 PHE 0.014 0.001 PHE B 372 TYR 0.018 0.001 TYR C 125 ARG 0.010 0.001 ARG E 138 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 1502) hydrogen bonds : angle 3.61463 ( 4359) covalent geometry : bond 0.00270 (23678) covalent geometry : angle 0.52567 (31994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 379 time to evaluate : 2.606 Fit side-chains revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8108 (m-30) cc_final: 0.7906 (m-30) REVERT: A 142 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8743 (ttt-90) REVERT: A 150 LYS cc_start: 0.7753 (tptp) cc_final: 0.7414 (pptt) REVERT: A 262 MET cc_start: 0.8088 (tpp) cc_final: 0.7883 (tpp) REVERT: A 275 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 311 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: A 313 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 546 LYS cc_start: 0.7730 (tptt) cc_final: 0.7519 (pttp) REVERT: A 594 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7984 (ttmm) REVERT: A 726 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7970 (tpp80) REVERT: A 745 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8336 (mmm160) REVERT: A 1137 VAL cc_start: 0.8612 (p) cc_final: 0.8298 (m) REVERT: A 1216 ASP cc_start: 0.7998 (m-30) cc_final: 0.7776 (m-30) REVERT: B 57 VAL cc_start: 0.8724 (t) cc_final: 0.8453 (t) REVERT: B 444 GLU cc_start: 0.7876 (pp20) cc_final: 0.7671 (pt0) REVERT: B 940 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 944 ASP cc_start: 0.8061 (m-30) cc_final: 0.7855 (m-30) REVERT: C 37 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7702 (mp) REVERT: C 78 VAL cc_start: 0.7293 (p) cc_final: 0.6977 (m) REVERT: C 167 GLN cc_start: 0.7091 (tp40) cc_final: 0.6625 (pp30) REVERT: E 3 GLU cc_start: 0.7293 (pm20) cc_final: 0.7058 (tp30) REVERT: E 36 ASN cc_start: 0.8567 (t0) cc_final: 0.7959 (t160) REVERT: E 39 GLN cc_start: 0.7104 (mp10) cc_final: 0.6887 (mp10) REVERT: E 40 SER cc_start: 0.7076 (OUTLIER) cc_final: 0.6826 (p) REVERT: F 45 MET cc_start: 0.7263 (tpp) cc_final: 0.6760 (tmm) REVERT: F 90 PHE cc_start: 0.8015 (t80) cc_final: 0.7532 (t80) REVERT: F 122 ASP cc_start: 0.8264 (t0) cc_final: 0.7972 (t0) outliers start: 53 outliers final: 11 residues processed: 405 average time/residue: 1.6441 time to fit residues: 749.4696 Evaluate side-chains 340 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 324 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 155 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 132 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 109 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 381 GLN A 505 ASN A 637 GLN A 709 GLN A 830 HIS A 884 GLN B 313 ASN E 71 ASN E 74 GLN F 162 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090560 restraints weight = 35514.719| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.62 r_work: 0.3087 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23678 Z= 0.175 Angle : 0.543 6.724 31994 Z= 0.285 Chirality : 0.040 0.233 3615 Planarity : 0.004 0.056 4073 Dihedral : 6.158 151.655 3141 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.55 % Allowed : 12.77 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.16), residues: 2830 helix: 2.61 (0.12), residues: 1916 sheet: -0.80 (0.50), residues: 78 loop : 0.09 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 646 HIS 0.005 0.001 HIS B 339 PHE 0.021 0.002 PHE B1002 TYR 0.021 0.001 TYR B 930 ARG 0.008 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05475 ( 1502) hydrogen bonds : angle 3.61128 ( 4359) covalent geometry : bond 0.00415 (23678) covalent geometry : angle 0.54294 (31994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8142 (m-30) cc_final: 0.7920 (m-30) REVERT: A 127 TYR cc_start: 0.8648 (m-10) cc_final: 0.8361 (m-10) REVERT: A 546 LYS cc_start: 0.7776 (tptt) cc_final: 0.7499 (pttp) REVERT: A 594 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8103 (ttmm) REVERT: A 745 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8522 (mmm160) REVERT: A 1137 VAL cc_start: 0.8958 (p) cc_final: 0.8593 (m) REVERT: A 1216 ASP cc_start: 0.8127 (m-30) cc_final: 0.7908 (m-30) REVERT: B 342 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8718 (mtt-85) REVERT: B 414 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8178 (mm-30) REVERT: B 940 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 944 ASP cc_start: 0.8085 (m-30) cc_final: 0.7859 (m-30) REVERT: B 1057 GLU cc_start: 0.8364 (tt0) cc_final: 0.8137 (mm-30) REVERT: C 62 PHE cc_start: 0.7736 (t80) cc_final: 0.7492 (m-80) REVERT: C 78 VAL cc_start: 0.7560 (p) cc_final: 0.7168 (m) REVERT: C 167 GLN cc_start: 0.7198 (tp40) cc_final: 0.6715 (pp30) REVERT: D 49 THR cc_start: 0.8901 (m) cc_final: 0.8651 (t) REVERT: E 36 ASN cc_start: 0.8556 (t0) cc_final: 0.7884 (t0) REVERT: E 39 GLN cc_start: 0.7408 (mp10) cc_final: 0.7167 (mp10) REVERT: F 66 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7235 (ptt90) REVERT: F 90 PHE cc_start: 0.8247 (t80) cc_final: 0.7716 (t80) outliers start: 66 outliers final: 19 residues processed: 385 average time/residue: 1.5301 time to fit residues: 667.3204 Evaluate side-chains 341 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 865 GLU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 206 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 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 62 GLN A 205 GLN A 505 ASN B 313 ASN B 391 ASN B 522 HIS D 51 ASN F 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090633 restraints weight = 35970.828| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.64 r_work: 0.3090 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23678 Z= 0.137 Angle : 0.510 7.630 31994 Z= 0.265 Chirality : 0.038 0.187 3615 Planarity : 0.004 0.049 4073 Dihedral : 6.140 154.007 3141 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.12 % Allowed : 15.08 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.16), residues: 2830 helix: 2.62 (0.12), residues: 1907 sheet: -0.82 (0.50), residues: 78 loop : 0.06 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.006 0.001 HIS C 60 PHE 0.019 0.001 PHE A 391 TYR 0.022 0.001 TYR B 930 ARG 0.008 0.000 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 1502) hydrogen bonds : angle 3.52527 ( 4359) covalent geometry : bond 0.00317 (23678) covalent geometry : angle 0.50969 (31994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 337 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8124 (m-30) cc_final: 0.7891 (m-30) REVERT: A 127 TYR cc_start: 0.8683 (m-10) cc_final: 0.8388 (m-10) REVERT: A 135 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7761 (ttt-90) REVERT: A 190 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6712 (mpp-170) REVERT: A 208 GLN cc_start: 0.8140 (tp40) cc_final: 0.7844 (tp-100) REVERT: A 211 SER cc_start: 0.8751 (t) cc_final: 0.8293 (m) REVERT: A 275 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 324 HIS cc_start: 0.8993 (m90) cc_final: 0.8725 (m90) REVERT: A 546 LYS cc_start: 0.7767 (tptt) cc_final: 0.7502 (pttp) REVERT: A 565 MET cc_start: 0.8665 (mtm) cc_final: 0.8440 (mtm) REVERT: A 594 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8159 (ttmm) REVERT: A 1084 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: A 1094 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: A 1216 ASP cc_start: 0.8173 (m-30) cc_final: 0.7965 (m-30) REVERT: B 57 VAL cc_start: 0.8630 (t) cc_final: 0.8376 (t) REVERT: B 342 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8580 (mtt-85) REVERT: B 392 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7753 (tmm) REVERT: B 555 GLN cc_start: 0.8603 (mt0) cc_final: 0.8337 (mt0) REVERT: B 940 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 1057 GLU cc_start: 0.8367 (tt0) cc_final: 0.8083 (mm-30) REVERT: C 62 PHE cc_start: 0.7711 (t80) cc_final: 0.7433 (m-80) REVERT: C 78 VAL cc_start: 0.7556 (p) cc_final: 0.7208 (m) REVERT: C 86 LYS cc_start: 0.7414 (mmtm) cc_final: 0.7148 (mmmt) REVERT: C 164 LYS cc_start: 0.8219 (tmmm) cc_final: 0.8015 (tmmm) REVERT: C 167 GLN cc_start: 0.7191 (tp40) cc_final: 0.6686 (pp30) REVERT: E 36 ASN cc_start: 0.8381 (t0) cc_final: 0.7871 (t0) REVERT: E 39 GLN cc_start: 0.7290 (mp10) cc_final: 0.7059 (mp10) REVERT: F 45 MET cc_start: 0.7547 (tpp) cc_final: 0.6837 (tmm) REVERT: F 90 PHE cc_start: 0.8313 (t80) cc_final: 0.7861 (t80) outliers start: 55 outliers final: 18 residues processed: 370 average time/residue: 1.5762 time to fit residues: 656.8155 Evaluate side-chains 349 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 255 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 505 ASN B 313 ASN B 555 GLN F 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.092001 restraints weight = 35896.439| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.66 r_work: 0.3115 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 23678 Z= 0.113 Angle : 0.491 8.736 31994 Z= 0.254 Chirality : 0.037 0.201 3615 Planarity : 0.003 0.049 4073 Dihedral : 6.112 158.844 3141 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.08 % Allowed : 16.05 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.16), residues: 2830 helix: 2.67 (0.12), residues: 1922 sheet: -0.69 (0.51), residues: 78 loop : 0.07 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.005 0.001 HIS C 60 PHE 0.018 0.001 PHE A 391 TYR 0.022 0.001 TYR B 930 ARG 0.010 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 1502) hydrogen bonds : angle 3.44837 ( 4359) covalent geometry : bond 0.00246 (23678) covalent geometry : angle 0.49150 (31994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8151 (m-30) cc_final: 0.7902 (m-30) REVERT: A 127 TYR cc_start: 0.8701 (m-10) cc_final: 0.8367 (m-10) REVERT: A 135 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7826 (ttt-90) REVERT: A 190 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6670 (mpp80) REVERT: A 208 GLN cc_start: 0.8090 (tp40) cc_final: 0.7800 (tp-100) REVERT: A 211 SER cc_start: 0.8760 (t) cc_final: 0.8321 (m) REVERT: A 324 HIS cc_start: 0.8919 (m90) cc_final: 0.8701 (m90) REVERT: A 546 LYS cc_start: 0.7749 (tptt) cc_final: 0.7477 (pttp) REVERT: A 594 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8096 (ttmm) REVERT: A 876 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6694 (mt0) REVERT: A 1216 ASP cc_start: 0.8168 (m-30) cc_final: 0.7939 (m-30) REVERT: B 57 VAL cc_start: 0.8611 (t) cc_final: 0.8397 (t) REVERT: B 728 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: B 940 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7524 (mt-10) REVERT: B 1057 GLU cc_start: 0.8344 (tt0) cc_final: 0.8049 (mm-30) REVERT: C 62 PHE cc_start: 0.7659 (t80) cc_final: 0.7389 (m-80) REVERT: C 78 VAL cc_start: 0.7472 (p) cc_final: 0.7103 (m) REVERT: C 86 LYS cc_start: 0.7439 (mmtm) cc_final: 0.7216 (mmmt) REVERT: C 167 GLN cc_start: 0.7101 (tp40) cc_final: 0.6643 (pp30) REVERT: E 36 ASN cc_start: 0.8359 (t0) cc_final: 0.7950 (t0) REVERT: E 39 GLN cc_start: 0.7157 (mp10) cc_final: 0.6904 (mp10) REVERT: F 45 MET cc_start: 0.7557 (tpp) cc_final: 0.6992 (tmm) REVERT: F 90 PHE cc_start: 0.8239 (t80) cc_final: 0.7796 (t80) outliers start: 54 outliers final: 15 residues processed: 379 average time/residue: 1.8240 time to fit residues: 782.3062 Evaluate side-chains 340 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 322 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 73 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 505 ASN A 884 GLN B 313 ASN B 945 HIS B1093 GLN F 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086398 restraints weight = 35971.471| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.71 r_work: 0.3006 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23678 Z= 0.222 Angle : 0.584 9.131 31994 Z= 0.303 Chirality : 0.041 0.222 3615 Planarity : 0.004 0.051 4073 Dihedral : 6.140 150.457 3141 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.58 % Allowed : 15.90 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2830 helix: 2.35 (0.12), residues: 1925 sheet: -0.86 (0.51), residues: 78 loop : -0.04 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 16 HIS 0.005 0.001 HIS A1128 PHE 0.023 0.002 PHE B1002 TYR 0.029 0.002 TYR A 688 ARG 0.009 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.06007 ( 1502) hydrogen bonds : angle 3.69369 ( 4359) covalent geometry : bond 0.00539 (23678) covalent geometry : angle 0.58363 (31994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6728 (mpp-170) REVERT: A 208 GLN cc_start: 0.8228 (tp40) cc_final: 0.7971 (tp-100) REVERT: A 211 SER cc_start: 0.8767 (t) cc_final: 0.8344 (m) REVERT: A 275 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (t0) REVERT: A 546 LYS cc_start: 0.7794 (tptt) cc_final: 0.7474 (pttp) REVERT: A 594 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8234 (ttmm) REVERT: A 876 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6816 (mt0) REVERT: A 1094 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: B 392 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7669 (tmm) REVERT: B 728 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: C 78 VAL cc_start: 0.7837 (p) cc_final: 0.7488 (m) REVERT: C 86 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7006 (mmmm) REVERT: C 167 GLN cc_start: 0.7111 (tp40) cc_final: 0.6627 (pp30) REVERT: D 62 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: E 36 ASN cc_start: 0.8407 (t0) cc_final: 0.8064 (t0) REVERT: E 39 GLN cc_start: 0.7585 (mp10) cc_final: 0.7336 (mp10) REVERT: F 90 PHE cc_start: 0.8369 (t80) cc_final: 0.7838 (t80) outliers start: 67 outliers final: 23 residues processed: 366 average time/residue: 1.8585 time to fit residues: 772.0045 Evaluate side-chains 339 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 865 GLU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 178 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 216 ASN A 505 ASN A 734 GLN A 884 GLN B 313 ASN B 555 GLN B 945 HIS F 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089829 restraints weight = 35926.776| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.68 r_work: 0.3073 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23678 Z= 0.121 Angle : 0.519 10.262 31994 Z= 0.269 Chirality : 0.037 0.215 3615 Planarity : 0.004 0.050 4073 Dihedral : 6.138 157.826 3141 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.97 % Allowed : 17.44 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.16), residues: 2830 helix: 2.53 (0.12), residues: 1929 sheet: -0.90 (0.52), residues: 78 loop : 0.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.005 0.001 HIS A1058 PHE 0.018 0.001 PHE A 391 TYR 0.024 0.001 TYR A 688 ARG 0.009 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 1502) hydrogen bonds : angle 3.55575 ( 4359) covalent geometry : bond 0.00257 (23678) covalent geometry : angle 0.51931 (31994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7836 (ttt-90) REVERT: A 208 GLN cc_start: 0.8130 (tp40) cc_final: 0.7856 (tp-100) REVERT: A 211 SER cc_start: 0.8742 (t) cc_final: 0.8327 (m) REVERT: A 546 LYS cc_start: 0.7732 (tptt) cc_final: 0.7450 (pttp) REVERT: A 594 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8157 (ttmm) REVERT: A 610 GLU cc_start: 0.8150 (mp0) cc_final: 0.7870 (mp0) REVERT: A 876 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: B 57 VAL cc_start: 0.8595 (t) cc_final: 0.8385 (t) REVERT: B 392 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: B 414 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 555 GLN cc_start: 0.8533 (mt0) cc_final: 0.8332 (mt0) REVERT: B 728 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: B 940 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 62 PHE cc_start: 0.7645 (t80) cc_final: 0.7437 (m-80) REVERT: C 78 VAL cc_start: 0.7637 (p) cc_final: 0.7261 (m) REVERT: C 86 LYS cc_start: 0.7475 (mmtm) cc_final: 0.7063 (mmmm) REVERT: C 167 GLN cc_start: 0.7108 (tp40) cc_final: 0.6667 (pp30) REVERT: D 61 ILE cc_start: 0.8622 (tp) cc_final: 0.8363 (tt) REVERT: E 36 ASN cc_start: 0.8445 (t0) cc_final: 0.8052 (t0) REVERT: E 39 GLN cc_start: 0.7358 (mp10) cc_final: 0.7090 (mp10) REVERT: F 45 MET cc_start: 0.7669 (tpp) cc_final: 0.7001 (tmm) REVERT: F 90 PHE cc_start: 0.8278 (t80) cc_final: 0.7852 (t80) REVERT: F 166 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7690 (mttm) REVERT: F 171 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7475 (mp0) outliers start: 51 outliers final: 20 residues processed: 361 average time/residue: 1.5164 time to fit residues: 618.4544 Evaluate side-chains 335 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 310 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 171 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 199 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 0.0030 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 216 ASN A 505 ASN A 884 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 313 ASN D 51 ASN F 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.086916 restraints weight = 35776.827| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.71 r_work: 0.3016 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23678 Z= 0.189 Angle : 0.570 11.143 31994 Z= 0.295 Chirality : 0.040 0.212 3615 Planarity : 0.004 0.051 4073 Dihedral : 6.118 151.891 3141 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.04 % Allowed : 17.79 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2830 helix: 2.36 (0.12), residues: 1933 sheet: -0.91 (0.51), residues: 78 loop : -0.09 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 16 HIS 0.018 0.001 HIS A1058 PHE 0.022 0.002 PHE A 391 TYR 0.025 0.002 TYR B 930 ARG 0.009 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 1502) hydrogen bonds : angle 3.67681 ( 4359) covalent geometry : bond 0.00453 (23678) covalent geometry : angle 0.56985 (31994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 318 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8238 (tp40) cc_final: 0.7990 (tp-100) REVERT: A 211 SER cc_start: 0.8743 (t) cc_final: 0.8339 (m) REVERT: A 274 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7727 (mtt) REVERT: A 303 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: A 528 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 546 LYS cc_start: 0.7783 (tptt) cc_final: 0.7438 (pttp) REVERT: A 594 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8216 (ttmm) REVERT: A 875 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.4837 (p90) REVERT: A 876 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: B 57 VAL cc_start: 0.8651 (t) cc_final: 0.8421 (t) REVERT: B 392 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: B 728 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: C 78 VAL cc_start: 0.7761 (p) cc_final: 0.7407 (m) REVERT: C 86 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7143 (mmmt) REVERT: C 167 GLN cc_start: 0.7108 (tp40) cc_final: 0.6645 (pp30) REVERT: D 61 ILE cc_start: 0.8682 (tp) cc_final: 0.8414 (tt) REVERT: E 36 ASN cc_start: 0.8394 (t0) cc_final: 0.8101 (t0) REVERT: E 39 GLN cc_start: 0.7567 (mp10) cc_final: 0.7263 (mp10) REVERT: F 45 MET cc_start: 0.7679 (tpp) cc_final: 0.7039 (tmm) REVERT: F 90 PHE cc_start: 0.8373 (t80) cc_final: 0.7860 (t80) REVERT: F 171 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7452 (mp0) outliers start: 53 outliers final: 23 residues processed: 352 average time/residue: 1.5659 time to fit residues: 625.4924 Evaluate side-chains 338 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 875 PHE Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 171 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 21 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 279 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 214 optimal weight: 0.0570 chunk 180 optimal weight: 0.8980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 216 ASN A 505 ASN A 884 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN D 51 ASN F 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.089023 restraints weight = 35853.808| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.72 r_work: 0.3055 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23678 Z= 0.125 Angle : 0.540 11.697 31994 Z= 0.278 Chirality : 0.037 0.205 3615 Planarity : 0.004 0.050 4073 Dihedral : 6.117 156.243 3141 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.70 % Allowed : 18.40 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.16), residues: 2830 helix: 2.46 (0.12), residues: 1933 sheet: -0.84 (0.52), residues: 78 loop : -0.04 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.007 0.001 HIS A1058 PHE 0.018 0.001 PHE A 391 TYR 0.023 0.001 TYR B 930 ARG 0.009 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 1502) hydrogen bonds : angle 3.60609 ( 4359) covalent geometry : bond 0.00276 (23678) covalent geometry : angle 0.54039 (31994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 318 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8185 (tp40) cc_final: 0.7916 (tp-100) REVERT: A 211 SER cc_start: 0.8702 (t) cc_final: 0.8305 (m) REVERT: A 303 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: A 546 LYS cc_start: 0.7768 (tptt) cc_final: 0.7500 (pttp) REVERT: A 594 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8159 (ttmm) REVERT: A 876 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6792 (mt0) REVERT: B 57 VAL cc_start: 0.8611 (t) cc_final: 0.8404 (t) REVERT: B 525 MET cc_start: 0.8636 (tpp) cc_final: 0.8407 (mmp) REVERT: B 728 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: B 940 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 78 VAL cc_start: 0.7679 (p) cc_final: 0.7281 (m) REVERT: C 86 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7141 (mmmt) REVERT: C 167 GLN cc_start: 0.7102 (tp40) cc_final: 0.6645 (pp30) REVERT: D 61 ILE cc_start: 0.8633 (tp) cc_final: 0.8372 (tt) REVERT: E 36 ASN cc_start: 0.8416 (t0) cc_final: 0.8110 (t0) REVERT: F 45 MET cc_start: 0.7734 (tpp) cc_final: 0.7125 (tmm) REVERT: F 66 ARG cc_start: 0.8064 (pmt-80) cc_final: 0.7834 (pmt-80) REVERT: F 90 PHE cc_start: 0.8308 (t80) cc_final: 0.7863 (t80) REVERT: F 171 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7451 (mp0) outliers start: 44 outliers final: 17 residues processed: 344 average time/residue: 1.6225 time to fit residues: 631.7683 Evaluate side-chains 325 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 136 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 216 ASN A 505 ASN A 884 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089105 restraints weight = 36049.816| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.73 r_work: 0.3057 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23678 Z= 0.130 Angle : 0.548 12.253 31994 Z= 0.281 Chirality : 0.038 0.204 3615 Planarity : 0.004 0.050 4073 Dihedral : 6.057 155.066 3141 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.20 % Allowed : 18.98 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.16), residues: 2830 helix: 2.50 (0.12), residues: 1926 sheet: -0.86 (0.51), residues: 78 loop : -0.06 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.007 0.001 HIS A1058 PHE 0.019 0.001 PHE A 391 TYR 0.024 0.001 TYR B 930 ARG 0.010 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 1502) hydrogen bonds : angle 3.59233 ( 4359) covalent geometry : bond 0.00297 (23678) covalent geometry : angle 0.54766 (31994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5660 Ramachandran restraints generated. 2830 Oldfield, 0 Emsley, 2830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 309 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8172 (tp40) cc_final: 0.7894 (tp-100) REVERT: A 211 SER cc_start: 0.8661 (t) cc_final: 0.8291 (m) REVERT: A 303 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 546 LYS cc_start: 0.7760 (tptt) cc_final: 0.7508 (pttp) REVERT: A 594 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8167 (ttmm) REVERT: A 876 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: B 525 MET cc_start: 0.8614 (tpp) cc_final: 0.8398 (mmp) REVERT: B 728 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: B 940 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 78 VAL cc_start: 0.7648 (p) cc_final: 0.7248 (m) REVERT: C 86 LYS cc_start: 0.7429 (mmtm) cc_final: 0.7136 (mmmt) REVERT: C 167 GLN cc_start: 0.7106 (tp40) cc_final: 0.6635 (pp30) REVERT: D 44 ARG cc_start: 0.8727 (mpt-90) cc_final: 0.8484 (mpt180) REVERT: D 61 ILE cc_start: 0.8618 (tp) cc_final: 0.8363 (tt) REVERT: E 36 ASN cc_start: 0.8396 (t0) cc_final: 0.8080 (t0) REVERT: F 45 MET cc_start: 0.7752 (tpp) cc_final: 0.7146 (tmm) REVERT: F 90 PHE cc_start: 0.8290 (t80) cc_final: 0.7844 (t80) REVERT: F 171 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7467 (mp0) outliers start: 31 outliers final: 16 residues processed: 329 average time/residue: 1.7662 time to fit residues: 660.0260 Evaluate side-chains 321 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 303 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 452 CYS Chi-restraints excluded: chain B residue 728 GLN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 233 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 505 ASN A 884 GLN A1012 GLN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089968 restraints weight = 35923.675| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.73 r_work: 0.3070 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23678 Z= 0.119 Angle : 0.551 13.766 31994 Z= 0.281 Chirality : 0.037 0.206 3615 Planarity : 0.004 0.050 4073 Dihedral : 6.054 155.791 3141 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.20 % Allowed : 19.10 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.16), residues: 2830 helix: 2.54 (0.12), residues: 1928 sheet: -0.87 (0.51), residues: 78 loop : -0.06 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.006 0.001 HIS A1058 PHE 0.017 0.001 PHE A 391 TYR 0.024 0.001 TYR B 930 ARG 0.009 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1502) hydrogen bonds : angle 3.57958 ( 4359) covalent geometry : bond 0.00261 (23678) covalent geometry : angle 0.55114 (31994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21738.92 seconds wall clock time: 379 minutes 29.20 seconds (22769.20 seconds total)