Starting phenix.real_space_refine on Mon Apr 15 09:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_40659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_40659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_40659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_40659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/04_2024/8soj_40659.pdb" } 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 Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 969": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.15, per 1000 atoms: 0.41 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 - 3.50 Amino acid : False - 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: 25.37 Conformation dependent library (CDL) restraints added in 3.7 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: 3.17 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: 15.25 Time building geometry restraints manager: 26.11 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: 96.59 - 104.09: 347 104.09 - 111.59: 39784 111.59 - 119.08: 8634 119.08 - 126.58: 14127 126.58 - 134.08: 329 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 1.850 nonbonded pdb=" OD1 ASP A 137 " pdb=" HG1 THR A 139 " model vdw 1.635 1.850 nonbonded pdb=" OD2 ASP D 561 " pdb=" H PHE D 565 " model vdw 1.640 1.850 nonbonded pdb=" OD1 ASP D 617 " pdb="HD21 ASN D 618 " model vdw 1.640 1.850 ... (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 ========== 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: 2.050 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: 0.480 Extract box with map and model: 10.800 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 112.400 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.930 ------------------------------------------------------------------------------- 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 17613 Z= 0.211 Angle : 0.642 5.615 23947 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 277 time to evaluate : 2.692 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: 0.8506 time to fit residues: 342.0647 Evaluate side-chains 159 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17613 Z= 0.235 Angle : 0.611 6.223 23947 Z= 0.317 Chirality : 0.041 0.169 2730 Planarity : 0.005 0.055 3086 Dihedral : 6.388 68.192 2386 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.40 % Allowed : 7.97 % Favored : 90.63 % 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: -0.36 (0.21), residues: 534 sheet: -1.26 (0.21), residues: 513 loop : -1.15 (0.18), residues: 1134 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 A 22 TYR 0.016 0.001 TYR A 385 ARG 0.008 0.000 ARG C 27 *********************** 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 184 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 2.616 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: A 300 MET cc_start: 0.8011 (ptm) cc_final: 0.7702 (ptm) REVERT: A 892 THR cc_start: 0.7282 (m) cc_final: 0.7009 (m) REVERT: A 1078 GLU cc_start: 0.6413 (tm-30) cc_final: 0.6008 (tm-30) REVERT: A 1087 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 1093 VAL cc_start: 0.9152 (m) cc_final: 0.8940 (p) REVERT: B 721 MET cc_start: 0.4014 (mpp) cc_final: 0.3722 (mmm) REVERT: D 238 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.5843 (m-80) REVERT: D 327 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.5882 (tt0) REVERT: D 360 TYR cc_start: 0.7554 (m-80) cc_final: 0.7167 (m-80) REVERT: D 575 MET cc_start: 0.7717 (mmm) cc_final: 0.7379 (mmm) outliers start: 27 outliers final: 21 residues processed: 177 average time/residue: 0.7757 time to fit residues: 199.6945 Evaluate side-chains 162 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER 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 238 PHE Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 576 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17613 Z= 0.306 Angle : 0.591 5.953 23947 Z= 0.308 Chirality : 0.041 0.167 2730 Planarity : 0.005 0.056 3086 Dihedral : 6.079 69.688 2384 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.76 % Allowed : 8.80 % Favored : 89.44 % 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: -1.38 (0.18), residues: 2181 helix: 0.03 (0.22), residues: 534 sheet: -1.43 (0.21), residues: 512 loop : -1.06 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 13 HIS 0.005 0.001 HIS C 48 PHE 0.016 0.002 PHE B 627 TYR 0.018 0.001 TYR A 385 ARG 0.004 0.000 ARG A 392 *********************** 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 176 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 2.842 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: A 300 MET cc_start: 0.7937 (ptm) cc_final: 0.7584 (ptm) REVERT: A 455 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: A 892 THR cc_start: 0.7364 (m) cc_final: 0.7091 (m) REVERT: A 1078 GLU cc_start: 0.6246 (tm-30) cc_final: 0.5769 (tm-30) REVERT: A 1087 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 1163 ARG cc_start: 0.5969 (tpt170) cc_final: 0.5357 (mmm160) REVERT: B 721 MET cc_start: 0.4052 (mpp) cc_final: 0.3740 (mmm) REVERT: D 209 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6673 (p-80) REVERT: D 360 TYR cc_start: 0.7692 (m-80) cc_final: 0.7194 (m-10) REVERT: D 560 MET cc_start: 0.8318 (tmm) cc_final: 0.8097 (tmm) REVERT: D 575 MET cc_start: 0.7755 (mmm) cc_final: 0.7409 (mmm) outliers start: 34 outliers final: 26 residues processed: 170 average time/residue: 0.7607 time to fit residues: 189.0277 Evaluate side-chains 158 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 164 SER 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 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 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 294 SER Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 576 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 187 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17613 Z= 0.169 Angle : 0.540 6.508 23947 Z= 0.276 Chirality : 0.040 0.154 2730 Planarity : 0.004 0.057 3086 Dihedral : 5.562 63.803 2381 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.71 % Allowed : 9.37 % Favored : 88.92 % 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: 0.40 (0.23), residues: 535 sheet: -1.36 (0.22), residues: 499 loop : -0.87 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 13 HIS 0.004 0.001 HIS C 48 PHE 0.021 0.001 PHE A 969 TYR 0.015 0.001 TYR A 991 ARG 0.003 0.000 ARG A 927 *********************** 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 171 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 2.540 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: A 300 MET cc_start: 0.7937 (ptm) cc_final: 0.7580 (ptm) REVERT: A 426 ARG cc_start: 0.7707 (ttt-90) cc_final: 0.7365 (ttp80) REVERT: A 1078 GLU cc_start: 0.5994 (tm-30) cc_final: 0.5534 (tm-30) REVERT: A 1087 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 1093 VAL cc_start: 0.9159 (m) cc_final: 0.8927 (p) REVERT: A 1163 ARG cc_start: 0.5925 (tpt170) cc_final: 0.5306 (mmm160) REVERT: B 721 MET cc_start: 0.4188 (mpp) cc_final: 0.3702 (mmm) REVERT: D 185 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.5256 (t0) REVERT: D 209 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6702 (p-80) REVERT: D 575 MET cc_start: 0.7809 (mmm) cc_final: 0.7443 (mmm) outliers start: 33 outliers final: 23 residues processed: 164 average time/residue: 0.7925 time to fit residues: 189.9386 Evaluate side-chains 154 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 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 154 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 991 TYR 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 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 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 576 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.0570 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 188 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17613 Z= 0.149 Angle : 0.514 6.005 23947 Z= 0.261 Chirality : 0.039 0.149 2730 Planarity : 0.004 0.058 3086 Dihedral : 5.257 60.150 2381 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.50 % Allowed : 9.78 % Favored : 88.72 % 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: -0.85 (0.18), residues: 2181 helix: 0.68 (0.23), residues: 535 sheet: -1.26 (0.22), residues: 495 loop : -0.77 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 13 HIS 0.004 0.000 HIS C 48 PHE 0.030 0.001 PHE D 315 TYR 0.015 0.001 TYR A 991 ARG 0.002 0.000 ARG A 392 *********************** 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 169 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 2.268 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: 0.7946 (ptm) cc_final: 0.7588 (ptm) REVERT: A 1078 GLU cc_start: 0.5887 (tm-30) cc_final: 0.5392 (tm-30) REVERT: A 1093 VAL cc_start: 0.9162 (m) cc_final: 0.8925 (p) REVERT: A 1163 ARG cc_start: 0.5860 (tpt170) cc_final: 0.5255 (mmm160) REVERT: B 721 MET cc_start: 0.4224 (mpp) cc_final: 0.3778 (mmm) REVERT: D 575 MET cc_start: 0.7758 (mmm) cc_final: 0.7419 (mmm) outliers start: 29 outliers final: 25 residues processed: 160 average time/residue: 0.7778 time to fit residues: 182.3489 Evaluate side-chains 152 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 83 SER 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 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 991 TYR 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 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 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 0.2980 chunk 174 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 0.0870 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17613 Z= 0.173 Angle : 0.512 5.774 23947 Z= 0.260 Chirality : 0.039 0.150 2730 Planarity : 0.004 0.057 3086 Dihedral : 5.135 60.083 2381 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.76 % Allowed : 10.30 % Favored : 87.94 % 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: -0.78 (0.18), residues: 2181 helix: 0.81 (0.24), residues: 535 sheet: -1.25 (0.22), residues: 491 loop : -0.76 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 13 HIS 0.004 0.001 HIS C 48 PHE 0.027 0.001 PHE D 315 TYR 0.013 0.001 TYR A 991 ARG 0.003 0.000 ARG B 508 *********************** 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 172 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 2.816 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: A 300 MET cc_start: 0.7946 (ptm) cc_final: 0.7580 (ptm) REVERT: A 1078 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5403 (tm-30) REVERT: A 1087 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 1093 VAL cc_start: 0.9174 (m) cc_final: 0.8941 (p) REVERT: A 1163 ARG cc_start: 0.5988 (tpt90) cc_final: 0.5388 (mmm160) REVERT: B 634 MET cc_start: 0.6609 (ppp) cc_final: 0.6347 (ppp) REVERT: B 721 MET cc_start: 0.4146 (mpp) cc_final: 0.3663 (mmm) REVERT: C 45 MET cc_start: 0.3191 (ptt) cc_final: 0.2986 (mtm) REVERT: D 185 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5134 (t0) REVERT: D 360 TYR cc_start: 0.7689 (m-80) cc_final: 0.7303 (m-80) REVERT: D 575 MET cc_start: 0.7780 (mmm) cc_final: 0.7437 (mmm) outliers start: 34 outliers final: 28 residues processed: 164 average time/residue: 0.7561 time to fit residues: 185.3644 Evaluate side-chains 156 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 83 SER 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 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 932 THR 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 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 C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17613 Z= 0.404 Angle : 0.605 6.419 23947 Z= 0.314 Chirality : 0.041 0.161 2730 Planarity : 0.005 0.056 3086 Dihedral : 5.517 71.291 2381 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.76 % Allowed : 10.77 % Favored : 87.47 % 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: -1.09 (0.18), residues: 2181 helix: 0.78 (0.24), residues: 523 sheet: -1.55 (0.22), residues: 500 loop : -0.99 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1143 HIS 0.008 0.001 HIS A 178 PHE 0.019 0.002 PHE A 657 TYR 0.019 0.002 TYR A 385 ARG 0.006 0.001 ARG A 392 *********************** 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 154 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 2.728 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: A 300 MET cc_start: 0.7983 (ptm) cc_final: 0.7616 (ptm) REVERT: A 892 THR cc_start: 0.7380 (m) cc_final: 0.7115 (m) REVERT: A 1087 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 1163 ARG cc_start: 0.6184 (tpt170) cc_final: 0.5609 (mmm160) REVERT: B 721 MET cc_start: 0.4187 (mpp) cc_final: 0.3771 (mmm) REVERT: D 185 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5331 (t0) REVERT: D 360 TYR cc_start: 0.7823 (m-80) cc_final: 0.7401 (m-80) REVERT: D 575 MET cc_start: 0.7862 (mmm) cc_final: 0.7496 (mmm) outliers start: 34 outliers final: 29 residues processed: 147 average time/residue: 0.7550 time to fit residues: 164.8662 Evaluate side-chains 144 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 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 932 THR 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 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 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 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 588 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17613 Z= 0.170 Angle : 0.522 5.768 23947 Z= 0.265 Chirality : 0.039 0.145 2730 Planarity : 0.004 0.056 3086 Dihedral : 5.160 64.429 2379 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.60 % Allowed : 11.23 % Favored : 87.16 % 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: -0.94 (0.18), residues: 2181 helix: 0.87 (0.24), residues: 530 sheet: -1.50 (0.22), residues: 509 loop : -0.85 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.004 0.001 HIS A 968 PHE 0.014 0.001 PHE A1040 TYR 0.014 0.001 TYR A 385 ARG 0.004 0.000 ARG A1102 *********************** 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 147 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 2.830 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: A 892 THR cc_start: 0.7246 (m) cc_final: 0.6986 (m) REVERT: A 1078 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5483 (tm-30) REVERT: A 1087 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 1163 ARG cc_start: 0.6117 (tpt170) cc_final: 0.5553 (mmm160) REVERT: B 721 MET cc_start: 0.4274 (mpp) cc_final: 0.3596 (mmm) REVERT: D 185 ASP cc_start: 0.5593 (OUTLIER) cc_final: 0.5294 (t0) REVERT: D 258 MET cc_start: 0.4237 (ppp) cc_final: 0.3971 (ppp) REVERT: D 360 TYR cc_start: 0.7718 (m-80) cc_final: 0.7345 (m-80) REVERT: D 575 MET cc_start: 0.7825 (mmm) cc_final: 0.7473 (mmm) outliers start: 31 outliers final: 28 residues processed: 140 average time/residue: 0.7536 time to fit residues: 158.4454 Evaluate side-chains 145 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 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 931 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 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 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 153 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 184 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17613 Z= 0.268 Angle : 0.542 5.980 23947 Z= 0.277 Chirality : 0.039 0.152 2730 Planarity : 0.004 0.056 3086 Dihedral : 5.175 67.460 2379 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 11.34 % Favored : 87.01 % 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: -1.02 (0.18), residues: 2181 helix: 0.87 (0.24), residues: 531 sheet: -1.62 (0.21), residues: 528 loop : -0.88 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1143 HIS 0.004 0.001 HIS A 178 PHE 0.014 0.001 PHE A1040 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 392 *********************** 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 150 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 2.840 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: A 892 THR cc_start: 0.7260 (m) cc_final: 0.6999 (m) REVERT: A 991 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6653 (t80) REVERT: A 1087 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 1163 ARG cc_start: 0.6155 (tpt170) cc_final: 0.5607 (mmm160) REVERT: B 721 MET cc_start: 0.4232 (mpp) cc_final: 0.3715 (mmm) REVERT: C 2 MET cc_start: 0.7103 (ppp) cc_final: 0.5994 (ppp) REVERT: D 185 ASP cc_start: 0.5620 (OUTLIER) cc_final: 0.5379 (t0) REVERT: D 258 MET cc_start: 0.4540 (ppp) cc_final: 0.4169 (ppp) REVERT: D 360 TYR cc_start: 0.7787 (m-80) cc_final: 0.7395 (m-80) REVERT: D 575 MET cc_start: 0.7825 (mmm) cc_final: 0.7480 (mmm) outliers start: 32 outliers final: 23 residues processed: 142 average time/residue: 0.7564 time to fit residues: 161.3359 Evaluate side-chains 140 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 GLN 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 991 TYR 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 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 D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 216 optimal weight: 0.4980 chunk 198 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17613 Z= 0.193 Angle : 0.523 6.710 23947 Z= 0.265 Chirality : 0.039 0.147 2730 Planarity : 0.004 0.062 3086 Dihedral : 5.065 65.369 2377 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.35 % Allowed : 11.65 % Favored : 87.01 % 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: -0.93 (0.18), residues: 2181 helix: 0.95 (0.24), residues: 533 sheet: -1.56 (0.21), residues: 522 loop : -0.85 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1143 HIS 0.003 0.001 HIS C 48 PHE 0.013 0.001 PHE A1040 TYR 0.015 0.001 TYR C 35 ARG 0.014 0.000 ARG A 287 ********************** 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 141 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 2.965 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: A 287 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.8004 (ttp80) REVERT: A 892 THR cc_start: 0.7259 (m) cc_final: 0.7001 (m) REVERT: A 991 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6674 (t80) REVERT: A 1087 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 1163 ARG cc_start: 0.6087 (tpt170) cc_final: 0.5573 (mmm160) REVERT: B 721 MET cc_start: 0.4153 (mpp) cc_final: 0.3677 (mmm) REVERT: C 2 MET cc_start: 0.7136 (ppp) cc_final: 0.6034 (ppp) REVERT: D 185 ASP cc_start: 0.5578 (OUTLIER) cc_final: 0.5373 (t0) REVERT: D 258 MET cc_start: 0.4552 (ppp) cc_final: 0.4095 (ppp) REVERT: D 360 TYR cc_start: 0.7712 (m-80) cc_final: 0.7357 (m-80) REVERT: D 575 MET cc_start: 0.7813 (mmm) cc_final: 0.7472 (mmm) outliers start: 26 outliers final: 22 residues processed: 136 average time/residue: 0.7418 time to fit residues: 150.9300 Evaluate side-chains 138 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 GLN 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 991 TYR 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 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 D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.162997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128174 restraints weight = 98491.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120729 restraints weight = 103098.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.117969 restraints weight = 86371.203| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17613 Z= 0.322 Angle : 0.566 6.679 23947 Z= 0.289 Chirality : 0.040 0.156 2730 Planarity : 0.004 0.054 3086 Dihedral : 5.207 69.407 2377 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.35 % Allowed : 11.80 % Favored : 86.85 % 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: 0.90 (0.24), residues: 534 sheet: -1.68 (0.21), residues: 528 loop : -0.95 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1143 HIS 0.006 0.001 HIS A 178 PHE 0.015 0.002 PHE A 657 TYR 0.016 0.001 TYR A 385 ARG 0.011 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6231.98 seconds wall clock time: 112 minutes 11.71 seconds (6731.71 seconds total)