Starting phenix.real_space_refine on Sun Jun 29 17:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.map" model { file = "/net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soj_40659/06_2025/8soj_40659.cif" } resolution = 3.8 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 97 5.16 5 C 10946 2.51 5 N 2988 2.21 5 O 3190 1.98 5 H 17267 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34490 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 18090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 18090 Classifications: {'peptide': 1158} Link IDs: {'PCIS': 6, 'PTRANS': 88, 'TRANS': 1063} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 6797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6797 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 17, 'TRANS': 410} Chain breaks: 1 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1897 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 7704 Classifications: {'peptide': 490} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 468} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15506 SG CYS A1043 77.163 92.425 71.542 1.00 77.69 S ATOM 15548 SG CYS A1046 74.525 95.132 70.928 1.00 94.18 S ATOM 15684 SG CYS A1055 78.159 95.560 69.743 1.00 99.30 S ATOM 15784 SG CYS A1062 77.492 95.679 73.394 1.00110.01 S ATOM 30547 SG CYS D 382 64.666 100.722 150.923 1.00103.05 S ATOM 30594 SG CYS D 385 64.810 104.124 149.472 1.00108.66 S ATOM 32449 SG CYS D 503 68.060 102.141 150.888 1.00116.52 S ATOM 32499 SG CYS D 506 65.517 103.834 153.110 1.00119.78 S Time building chain proxies: 16.00, per 1000 atoms: 0.46 Number of scatterers: 34490 At special positions: 0 Unit cell: (110.08, 140.18, 192.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 97 16.00 O 3190 8.00 N 2988 7.00 C 10946 6.00 H 17267 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.55 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 506 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 503 " Number of angles added : 12 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 26 sheets defined 29.5% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 37 through 53 removed outlier: 4.015A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.723A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.365A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 515 removed outlier: 3.907A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.825A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.541A pdb=" N LEU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.531A pdb=" N LEU A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.534A pdb=" N SER A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.692A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1018 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 4.185A pdb=" N ALA A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1095 " --> pdb=" O HIS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1112 Processing helix chain 'A' and resid 1136 through 1146 Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 506 through 528 Processing helix chain 'B' and resid 563 through 580 Proline residue: B 574 - end of helix Processing helix chain 'B' and resid 603 through 622 Processing helix chain 'B' and resid 629 through 634 Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 644 through 652 removed outlier: 3.558A pdb=" N HIS B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 657 through 680 Processing helix chain 'B' and resid 700 through 712 removed outlier: 3.530A pdb=" N ILE B 710 " --> pdb=" O LYS B 706 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 743 through 758 Processing helix chain 'C' and resid 11 through 17 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 212 through 217 removed outlier: 5.638A pdb=" N ASN D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.605A pdb=" N LYS D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.558A pdb=" N GLN D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 removed outlier: 3.612A pdb=" N ILE D 634 " --> pdb=" O GLU D 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 631 through 634' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 4.687A pdb=" N LEU A 114 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 181 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A 145 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 4.687A pdb=" N LEU A 114 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 113 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 204 removed outlier: 5.905A pdb=" N ILE A 201 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 318 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 203 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.791A pdb=" N TRP A 299 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 301 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 298 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 7.180A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 428 through 433 removed outlier: 3.528A pdb=" N ALA A 428 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 364 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 354 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N HIS A 407 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 356 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 596 removed outlier: 3.743A pdb=" N GLU A 662 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N SER A 629 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL A 690 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 692 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 633 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 592 through 596 removed outlier: 3.743A pdb=" N GLU A 662 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N SER A 629 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL A 690 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 692 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 633 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 632 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 621 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 781 removed outlier: 7.065A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 732 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 772 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER A 730 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN A 774 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 728 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 816 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 991 through 996 removed outlier: 6.507A pdb=" N ARG A 966 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL A 982 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP A 947 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 929 " --> pdb=" O ILE A 950 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N CYS A 928 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 907 " --> pdb=" O CYS A 928 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 930 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG A 905 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 932 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 898 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 970 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 900 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS A 968 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 902 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 966 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 6.934A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1194 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A1041 " --> pdb=" O CYS A1050 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER A1048 " --> pdb=" O CYS A1043 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A1051 " --> pdb=" O LYS A1054 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 6.934A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1194 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1175 through 1181 Processing sheet with id=AB8, first strand: chain 'B' and resid 429 through 430 removed outlier: 6.248A pdb=" N ALA B 430 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU B 463 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 534 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER B 540 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA B 552 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 542 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE B 550 " --> pdb=" O ARG B 542 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 544 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG B 548 " --> pdb=" O TYR B 544 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ARG B 548 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN B 488 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP B 492 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR B 554 " --> pdb=" O TRP B 492 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B 471 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 477 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL B 469 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 479 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.685A pdb=" N LYS B 441 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 626 through 628 Processing sheet with id=AC2, first strand: chain 'B' and resid 725 through 726 removed outlier: 3.768A pdb=" N MET B 764 " --> pdb=" O TYR B 767 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B 769 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER B 762 " --> pdb=" O THR B 769 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 44 through 45 removed outlier: 6.300A pdb=" N GLU C 78 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 91 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN C 80 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL C 89 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN C 82 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 87 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.660A pdb=" N SER D 260 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP D 219 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU D 265 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 221 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 178 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU D 173 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU D 180 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS D 171 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS D 182 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 274 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AC6, first strand: chain 'D' and resid 387 through 389 removed outlier: 3.557A pdb=" N ASP D 561 " --> pdb=" O PHE D 542 " (cutoff:3.500A) removed outlier: 12.632A pdb=" N VAL D 554 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N TYR D 622 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU D 556 " --> pdb=" O TYR D 622 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE D 624 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D 558 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE D 606 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU D 366 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 549 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 368 " --> pdb=" O THR D 547 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 419 through 426 removed outlier: 3.660A pdb=" N ARG D 432 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 452 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU D 453 " --> pdb=" O ILE D 474 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 493 through 495 removed outlier: 3.579A pdb=" N LEU D 493 " --> pdb=" O HIS D 500 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 1890 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: 17.20 Time building geometry restraints manager: 10.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17190 1.03 - 1.23: 331 1.23 - 1.43: 6973 1.43 - 1.63: 10261 1.63 - 1.82: 125 Bond restraints: 34880 Sorted by residual: bond pdb=" N LYS B 723 " pdb=" H LYS B 723 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N ARG B 410 " pdb=" H ARG B 410 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CE LYS B 723 " pdb=" HE3 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" CE LYS B 723 " pdb=" HE2 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CB LYS B 723 " pdb=" HB2 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 34875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 62917 2.48 - 4.96: 291 4.96 - 7.44: 10 7.44 - 9.92: 1 9.92 - 12.41: 2 Bond angle restraints: 63221 Sorted by residual: angle pdb=" CA THR C 43 " pdb=" C THR C 43 " pdb=" O THR C 43 " ideal model delta sigma weight residual 121.40 116.63 4.77 1.13e+00 7.83e-01 1.78e+01 angle pdb=" CA THR B 769 " pdb=" C THR B 769 " pdb=" O THR B 769 " ideal model delta sigma weight residual 120.89 116.27 4.62 1.10e+00 8.26e-01 1.76e+01 angle pdb=" CA LEU C 56 " pdb=" C LEU C 56 " pdb=" O LEU C 56 " ideal model delta sigma weight residual 121.19 116.64 4.55 1.10e+00 8.26e-01 1.71e+01 angle pdb=" CA LEU C 34 " pdb=" C LEU C 34 " pdb=" O LEU C 34 " ideal model delta sigma weight residual 120.56 116.82 3.74 9.70e-01 1.06e+00 1.48e+01 angle pdb=" CA MET C 45 " pdb=" C MET C 45 " pdb=" O MET C 45 " ideal model delta sigma weight residual 121.55 117.77 3.78 1.06e+00 8.90e-01 1.27e+01 ... (remaining 63216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 15123 16.80 - 33.59: 870 33.59 - 50.39: 312 50.39 - 67.19: 157 67.19 - 83.99: 21 Dihedral angle restraints: 16483 sinusoidal: 9081 harmonic: 7402 Sorted by residual: dihedral pdb=" CA GLU A 951 " pdb=" C GLU A 951 " pdb=" N ASP A 952 " pdb=" CA ASP A 952 " ideal model delta harmonic sigma weight residual 180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLN D 157 " pdb=" C GLN D 157 " pdb=" N PRO D 158 " pdb=" CA PRO D 158 " ideal model delta harmonic sigma weight residual 180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG D 328 " pdb=" C ARG D 328 " pdb=" N CYS D 329 " pdb=" CA CYS D 329 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2166 0.047 - 0.094: 414 0.094 - 0.142: 138 0.142 - 0.189: 10 0.189 - 0.236: 2 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA VAL C 42 " pdb=" N VAL C 42 " pdb=" C VAL C 42 " pdb=" CB VAL C 42 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL C 55 " pdb=" N VAL C 55 " pdb=" C VAL C 55 " pdb=" CB VAL C 55 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LEU C 34 " pdb=" N LEU C 34 " pdb=" C LEU C 34 " pdb=" CB LEU C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 2727 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 31 " -0.527 9.50e-02 1.11e+02 3.85e-01 2.67e+03 pdb=" NE ARG C 31 " -0.149 2.00e-02 2.50e+03 pdb=" CZ ARG C 31 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 31 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 31 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG C 31 " 0.739 2.00e-02 2.50e+03 pdb="HH12 ARG C 31 " -0.689 2.00e-02 2.50e+03 pdb="HH21 ARG C 31 " 0.097 2.00e-02 2.50e+03 pdb="HH22 ARG C 31 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 54 " 0.242 2.00e-02 2.50e+03 2.87e-01 1.24e+03 pdb=" CD GLN C 54 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN C 54 " -0.225 2.00e-02 2.50e+03 pdb=" NE2 GLN C 54 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN C 54 " -0.432 2.00e-02 2.50e+03 pdb="HE22 GLN C 54 " 0.447 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 41 " -0.631 9.50e-02 1.11e+02 2.11e-01 4.95e+01 pdb=" NE ARG C 41 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG C 41 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 41 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 41 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG C 41 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 41 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG C 41 " -0.011 2.00e-02 2.50e+03 pdb="HH22 ARG C 41 " -0.000 2.00e-02 2.50e+03 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 255 1.96 - 2.62: 40371 2.62 - 3.28: 103688 3.28 - 3.94: 127248 3.94 - 4.60: 199661 Nonbonded interactions: 471223 Sorted by model distance: nonbonded pdb=" HG2 LYS B 723 " pdb=" HZ3 LYS B 723 " model vdw 1.297 2.270 nonbonded pdb=" OE2 GLU A 145 " pdb="HH22 ARG A 393 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASP A 137 " pdb=" HG1 THR A 139 " model vdw 1.635 2.450 nonbonded pdb=" OD2 ASP D 561 " pdb=" H PHE D 565 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP D 617 " pdb="HD21 ASN D 618 " model vdw 1.640 2.450 ... (remaining 471218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.530 Extract box with map and model: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 90.610 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.130 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 : 0.003 0.041 17621 Z= 0.171 Angle : 0.650 11.272 23959 Z= 0.356 Chirality : 0.043 0.236 2730 Planarity : 0.007 0.281 3086 Dihedral : 12.259 83.987 6558 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.04 % Favored : 94.73 % Rotamer: Outliers : 0.52 % Allowed : 5.38 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -2.25 (0.16), residues: 2181 helix: -1.46 (0.19), residues: 526 sheet: -1.15 (0.21), residues: 506 loop : -1.62 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 13 HIS 0.005 0.001 HIS A1091 PHE 0.015 0.001 PHE A1040 TYR 0.027 0.002 TYR B 767 ARG 0.007 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.16544 ( 674) hydrogen bonds : angle 7.84306 ( 1890) metal coordination : bond 0.00502 ( 8) metal coordination : angle 4.54316 ( 12) covalent geometry : bond 0.00321 (17613) covalent geometry : angle 0.64176 (23947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7912 (ptm) cc_final: 0.7681 (ptm) REVERT: A 892 THR cc_start: 0.7383 (m) cc_final: 0.7077 (m) REVERT: A 1078 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6215 (tm-30) REVERT: B 721 MET cc_start: 0.4031 (mpp) cc_final: 0.3549 (mmm) REVERT: D 327 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.5699 (tt0) REVERT: D 368 SER cc_start: 0.9051 (p) cc_final: 0.8660 (t) REVERT: D 575 MET cc_start: 0.7614 (mmm) cc_final: 0.7334 (mmm) outliers start: 10 outliers final: 7 residues processed: 286 average time/residue: 0.8773 time to fit residues: 353.1066 Evaluate side-chains 159 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN B 622 ASN D 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.167481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.133826 restraints weight = 98450.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.127106 restraints weight = 95257.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125882 restraints weight = 80056.209| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17621 Z= 0.148 Angle : 0.624 10.144 23959 Z= 0.320 Chirality : 0.042 0.167 2730 Planarity : 0.005 0.055 3086 Dihedral : 6.418 67.486 2386 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.29 % Allowed : 8.18 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.54 (0.17), residues: 2181 helix: -0.35 (0.21), residues: 534 sheet: -1.30 (0.22), residues: 472 loop : -1.16 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 13 HIS 0.006 0.001 HIS D 226 PHE 0.021 0.001 PHE A1040 TYR 0.015 0.001 TYR A 991 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 674) hydrogen bonds : angle 6.01887 ( 1890) metal coordination : bond 0.00619 ( 8) metal coordination : angle 4.66305 ( 12) covalent geometry : bond 0.00337 (17613) covalent geometry : angle 0.61504 (23947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7795 (ptm) cc_final: 0.7588 (ptm) REVERT: A 892 THR cc_start: 0.7189 (m) cc_final: 0.6904 (m) REVERT: A 1078 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6292 (tm-30) REVERT: A 1087 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 1093 VAL cc_start: 0.9123 (m) cc_final: 0.8897 (p) REVERT: B 721 MET cc_start: 0.4286 (mpp) cc_final: 0.4039 (mmm) REVERT: D 327 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.5861 (tt0) REVERT: D 575 MET cc_start: 0.7497 (mmm) cc_final: 0.7215 (mmm) outliers start: 25 outliers final: 20 residues processed: 176 average time/residue: 0.8146 time to fit residues: 211.2877 Evaluate side-chains 158 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 139 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.164250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.128489 restraints weight = 98470.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121623 restraints weight = 95044.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119148 restraints weight = 94528.808| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17621 Z= 0.265 Angle : 0.652 7.206 23959 Z= 0.339 Chirality : 0.042 0.170 2730 Planarity : 0.005 0.061 3086 Dihedral : 6.259 72.743 2384 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.76 % Allowed : 9.01 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.52 (0.17), residues: 2181 helix: -0.00 (0.22), residues: 527 sheet: -1.59 (0.22), residues: 483 loop : -1.16 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 13 HIS 0.007 0.001 HIS A 178 PHE 0.022 0.002 PHE B 627 TYR 0.020 0.002 TYR A 385 ARG 0.006 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 674) hydrogen bonds : angle 5.82111 ( 1890) metal coordination : bond 0.00592 ( 8) metal coordination : angle 4.01979 ( 12) covalent geometry : bond 0.00607 (17613) covalent geometry : angle 0.64629 (23947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7845 (ptm) cc_final: 0.7552 (ptm) REVERT: A 455 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 892 THR cc_start: 0.7309 (m) cc_final: 0.7026 (m) REVERT: A 1078 GLU cc_start: 0.6403 (tm-30) cc_final: 0.6138 (tm-30) REVERT: A 1087 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8676 (p) REVERT: A 1093 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 1163 ARG cc_start: 0.6043 (tpt170) cc_final: 0.5374 (mmm160) REVERT: B 721 MET cc_start: 0.4042 (mpp) cc_final: 0.3631 (mmm) REVERT: D 209 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6701 (p-80) REVERT: D 575 MET cc_start: 0.7640 (mmm) cc_final: 0.7357 (mmm) outliers start: 34 outliers final: 22 residues processed: 168 average time/residue: 0.7217 time to fit residues: 180.3435 Evaluate side-chains 150 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 141 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 35 optimal weight: 0.0070 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.165724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.128400 restraints weight = 98501.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120358 restraints weight = 89718.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.117746 restraints weight = 82687.289| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17621 Z= 0.143 Angle : 0.573 6.456 23959 Z= 0.292 Chirality : 0.040 0.160 2730 Planarity : 0.004 0.058 3086 Dihedral : 5.740 65.097 2381 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.60 % Allowed : 9.94 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.31 (0.18), residues: 2181 helix: 0.32 (0.23), residues: 535 sheet: -1.59 (0.23), residues: 476 loop : -1.06 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 13 HIS 0.005 0.001 HIS C 48 PHE 0.022 0.001 PHE D 315 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG B 569 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 674) hydrogen bonds : angle 5.49139 ( 1890) metal coordination : bond 0.00440 ( 8) metal coordination : angle 3.60867 ( 12) covalent geometry : bond 0.00329 (17613) covalent geometry : angle 0.56712 (23947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7917 (ptm) cc_final: 0.7540 (ptm) REVERT: A 892 THR cc_start: 0.7213 (m) cc_final: 0.6959 (m) REVERT: A 1078 GLU cc_start: 0.6172 (tm-30) cc_final: 0.5927 (tm-30) REVERT: A 1087 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 1093 VAL cc_start: 0.9161 (m) cc_final: 0.8872 (p) REVERT: A 1163 ARG cc_start: 0.5948 (tpt170) cc_final: 0.5328 (mmm160) REVERT: B 721 MET cc_start: 0.4128 (mpp) cc_final: 0.3749 (mmm) REVERT: D 209 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6765 (p-80) REVERT: D 575 MET cc_start: 0.7770 (mmm) cc_final: 0.7435 (mmm) outliers start: 31 outliers final: 24 residues processed: 154 average time/residue: 0.7679 time to fit residues: 176.2707 Evaluate side-chains 147 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 105 optimal weight: 0.2980 chunk 50 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.166305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115646 restraints weight = 98245.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115123 restraints weight = 80808.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.116851 restraints weight = 59827.468| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17621 Z= 0.113 Angle : 0.540 5.697 23959 Z= 0.274 Chirality : 0.040 0.145 2730 Planarity : 0.004 0.058 3086 Dihedral : 5.419 61.794 2381 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.86 % Allowed : 10.09 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.10 (0.18), residues: 2181 helix: 0.59 (0.23), residues: 535 sheet: -1.55 (0.22), residues: 488 loop : -0.92 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 PHE 0.013 0.001 PHE A1040 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 674) hydrogen bonds : angle 5.21642 ( 1890) metal coordination : bond 0.00346 ( 8) metal coordination : angle 3.08572 ( 12) covalent geometry : bond 0.00263 (17613) covalent geometry : angle 0.53589 (23947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7874 (ptm) cc_final: 0.7473 (ptm) REVERT: A 892 THR cc_start: 0.7232 (m) cc_final: 0.6972 (m) REVERT: A 903 LEU cc_start: 0.8741 (mt) cc_final: 0.8483 (mp) REVERT: A 1087 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 1093 VAL cc_start: 0.9148 (m) cc_final: 0.8906 (p) REVERT: A 1163 ARG cc_start: 0.5973 (tpt170) cc_final: 0.5380 (mmm160) REVERT: B 634 MET cc_start: 0.6667 (ppp) cc_final: 0.6444 (ppp) REVERT: B 721 MET cc_start: 0.4102 (mpp) cc_final: 0.3762 (mmm) REVERT: D 185 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5132 (t0) REVERT: D 209 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6717 (p-80) REVERT: D 575 MET cc_start: 0.7695 (mmm) cc_final: 0.7363 (mmm) outliers start: 36 outliers final: 25 residues processed: 159 average time/residue: 0.7040 time to fit residues: 167.1397 Evaluate side-chains 152 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 157 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.163647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119645 restraints weight = 97370.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119551 restraints weight = 87646.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122281 restraints weight = 67982.367| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17621 Z= 0.226 Angle : 0.586 5.632 23959 Z= 0.303 Chirality : 0.041 0.161 2730 Planarity : 0.005 0.055 3086 Dihedral : 5.517 69.130 2377 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 11.13 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.19 (0.18), residues: 2181 helix: 0.71 (0.23), residues: 523 sheet: -1.75 (0.22), residues: 491 loop : -0.99 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.006 0.001 HIS A 178 PHE 0.016 0.002 PHE A1040 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 674) hydrogen bonds : angle 5.33454 ( 1890) metal coordination : bond 0.00434 ( 8) metal coordination : angle 3.17401 ( 12) covalent geometry : bond 0.00528 (17613) covalent geometry : angle 0.58206 (23947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7685 (ptm) cc_final: 0.7404 (ptm) REVERT: A 892 THR cc_start: 0.7261 (m) cc_final: 0.6993 (m) REVERT: A 926 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.7115 (mtm-85) REVERT: A 991 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6740 (t80) REVERT: A 1087 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 1163 ARG cc_start: 0.6125 (tpt170) cc_final: 0.5543 (mmm160) REVERT: B 721 MET cc_start: 0.4353 (mpp) cc_final: 0.4074 (mmm) REVERT: D 185 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5098 (t0) REVERT: D 209 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6754 (p-80) REVERT: D 315 PHE cc_start: 0.7199 (t80) cc_final: 0.6962 (t80) REVERT: D 575 MET cc_start: 0.7654 (mmm) cc_final: 0.7359 (mmm) outliers start: 35 outliers final: 28 residues processed: 149 average time/residue: 0.7202 time to fit residues: 159.5811 Evaluate side-chains 145 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 588 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 198 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 HIS B 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.165088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119193 restraints weight = 98248.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.116756 restraints weight = 82790.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118044 restraints weight = 61954.874| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17621 Z= 0.122 Angle : 0.542 5.954 23959 Z= 0.274 Chirality : 0.040 0.149 2730 Planarity : 0.004 0.054 3086 Dihedral : 5.278 64.406 2377 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.45 % Allowed : 11.85 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.10 (0.18), residues: 2181 helix: 0.77 (0.24), residues: 530 sheet: -1.66 (0.22), residues: 489 loop : -0.96 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 469 HIS 0.004 0.001 HIS A 968 PHE 0.014 0.001 PHE A1040 TYR 0.016 0.001 TYR B 694 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 674) hydrogen bonds : angle 5.13834 ( 1890) metal coordination : bond 0.00325 ( 8) metal coordination : angle 2.99033 ( 12) covalent geometry : bond 0.00285 (17613) covalent geometry : angle 0.53788 (23947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7846 (ptm) cc_final: 0.7447 (ptm) REVERT: A 892 THR cc_start: 0.7196 (m) cc_final: 0.6940 (m) REVERT: A 903 LEU cc_start: 0.8906 (mt) cc_final: 0.8544 (mp) REVERT: A 991 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6604 (t80) REVERT: A 1087 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 1163 ARG cc_start: 0.6125 (tpt170) cc_final: 0.5571 (mmm160) REVERT: B 721 MET cc_start: 0.4189 (mpp) cc_final: 0.3907 (mmm) REVERT: D 209 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6796 (p-80) REVERT: D 315 PHE cc_start: 0.7284 (t80) cc_final: 0.7081 (t80) REVERT: D 575 MET cc_start: 0.7711 (mmm) cc_final: 0.7389 (mmm) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 0.7394 time to fit residues: 152.7385 Evaluate side-chains 139 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.164883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.131492 restraints weight = 98296.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122475 restraints weight = 96358.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121496 restraints weight = 92402.394| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17621 Z= 0.139 Angle : 0.537 6.359 23959 Z= 0.272 Chirality : 0.039 0.152 2730 Planarity : 0.004 0.050 3086 Dihedral : 5.134 64.551 2375 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.71 % Allowed : 11.59 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.08 (0.18), residues: 2181 helix: 0.82 (0.24), residues: 531 sheet: -1.66 (0.22), residues: 489 loop : -0.97 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 PHE 0.012 0.001 PHE A1040 TYR 0.014 0.001 TYR A 385 ARG 0.004 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 674) hydrogen bonds : angle 5.05403 ( 1890) metal coordination : bond 0.00314 ( 8) metal coordination : angle 2.93142 ( 12) covalent geometry : bond 0.00327 (17613) covalent geometry : angle 0.53344 (23947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7807 (ptm) cc_final: 0.7451 (ptm) REVERT: A 593 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (t) REVERT: A 892 THR cc_start: 0.7168 (m) cc_final: 0.6924 (m) REVERT: A 991 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 1087 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 1163 ARG cc_start: 0.6015 (tpt170) cc_final: 0.5461 (mmm160) REVERT: B 721 MET cc_start: 0.4260 (mpp) cc_final: 0.4012 (mmm) REVERT: D 185 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.5142 (t0) REVERT: D 209 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6762 (p-80) REVERT: D 258 MET cc_start: 0.4355 (ppp) cc_final: 0.3861 (ppp) REVERT: D 315 PHE cc_start: 0.7390 (t80) cc_final: 0.7160 (t80) REVERT: D 575 MET cc_start: 0.7697 (mmm) cc_final: 0.7415 (mmm) outliers start: 33 outliers final: 26 residues processed: 147 average time/residue: 0.7260 time to fit residues: 158.9945 Evaluate side-chains 145 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 39 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.165197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123010 restraints weight = 98242.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126304 restraints weight = 84474.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123646 restraints weight = 45385.254| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17621 Z= 0.125 Angle : 0.534 6.400 23959 Z= 0.269 Chirality : 0.039 0.151 2730 Planarity : 0.004 0.049 3086 Dihedral : 5.032 64.385 2375 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.76 % Allowed : 11.75 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -1.04 (0.18), residues: 2181 helix: 0.89 (0.24), residues: 531 sheet: -1.65 (0.22), residues: 489 loop : -0.95 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 PHE 0.012 0.001 PHE A1040 TYR 0.013 0.001 TYR A 385 ARG 0.005 0.000 ARG A 926 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 674) hydrogen bonds : angle 4.97543 ( 1890) metal coordination : bond 0.00299 ( 8) metal coordination : angle 2.89966 ( 12) covalent geometry : bond 0.00296 (17613) covalent geometry : angle 0.52975 (23947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7785 (ptm) cc_final: 0.7446 (ptm) REVERT: A 593 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (t) REVERT: A 892 THR cc_start: 0.7124 (m) cc_final: 0.6878 (m) REVERT: A 991 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 1087 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8644 (p) REVERT: A 1163 ARG cc_start: 0.6006 (tpt170) cc_final: 0.5476 (mmm160) REVERT: B 721 MET cc_start: 0.4222 (mpp) cc_final: 0.3999 (mmm) REVERT: D 185 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5072 (t0) REVERT: D 209 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6734 (p-80) REVERT: D 258 MET cc_start: 0.4476 (ppp) cc_final: 0.3956 (ppp) REVERT: D 315 PHE cc_start: 0.7262 (t80) cc_final: 0.7051 (t80) REVERT: D 575 MET cc_start: 0.7543 (mmm) cc_final: 0.7254 (mmm) outliers start: 34 outliers final: 26 residues processed: 142 average time/residue: 0.7438 time to fit residues: 159.3967 Evaluate side-chains 145 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.165172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.118878 restraints weight = 97851.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.118319 restraints weight = 83945.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120456 restraints weight = 63251.048| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17621 Z= 0.117 Angle : 0.528 6.602 23959 Z= 0.266 Chirality : 0.039 0.150 2730 Planarity : 0.004 0.048 3086 Dihedral : 4.948 63.405 2375 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.60 % Allowed : 11.80 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.98 (0.18), residues: 2181 helix: 0.97 (0.24), residues: 532 sheet: -1.62 (0.22), residues: 485 loop : -0.93 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 PHE 0.011 0.001 PHE A1040 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 674) hydrogen bonds : angle 4.87957 ( 1890) metal coordination : bond 0.00269 ( 8) metal coordination : angle 2.83246 ( 12) covalent geometry : bond 0.00277 (17613) covalent geometry : angle 0.52402 (23947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7764 (ptm) cc_final: 0.7429 (ptm) REVERT: A 593 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8687 (t) REVERT: A 892 THR cc_start: 0.7182 (m) cc_final: 0.6935 (m) REVERT: A 991 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6764 (t80) REVERT: A 1087 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 1163 ARG cc_start: 0.6047 (tpt170) cc_final: 0.5539 (mmm160) REVERT: D 185 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5022 (t0) REVERT: D 209 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6766 (p-80) REVERT: D 258 MET cc_start: 0.4496 (ppp) cc_final: 0.3958 (ppp) REVERT: D 575 MET cc_start: 0.7521 (mmm) cc_final: 0.7263 (mmm) outliers start: 31 outliers final: 24 residues processed: 145 average time/residue: 0.7327 time to fit residues: 160.5628 Evaluate side-chains 145 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.165689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128149 restraints weight = 98107.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.118597 restraints weight = 82937.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117315 restraints weight = 78416.812| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17621 Z= 0.102 Angle : 0.517 7.147 23959 Z= 0.258 Chirality : 0.039 0.148 2730 Planarity : 0.004 0.049 3086 Dihedral : 4.667 61.662 2371 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.40 % Allowed : 12.01 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.89 (0.18), residues: 2181 helix: 1.08 (0.24), residues: 534 sheet: -1.57 (0.22), residues: 492 loop : -0.88 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 PHE 0.038 0.001 PHE D 315 TYR 0.012 0.001 TYR A 991 ARG 0.005 0.000 ARG A 426 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 674) hydrogen bonds : angle 4.79702 ( 1890) metal coordination : bond 0.00254 ( 8) metal coordination : angle 2.80361 ( 12) covalent geometry : bond 0.00243 (17613) covalent geometry : angle 0.51346 (23947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10009.14 seconds wall clock time: 172 minutes 24.53 seconds (10344.53 seconds total)