Starting phenix.real_space_refine on Tue Nov 21 16:16:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/11_2023/8soj_40659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/11_2023/8soj_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_40659/11_2023/8soj_40659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/11_2023/8soj_40659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/11_2023/8soj_40659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8soj_40659/11_2023/8soj_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 15.07, per 1000 atoms: 0.44 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: 28.01 Conformation dependent library (CDL) restraints added in 3.9 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: 3.13 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: 14.78 Time building geometry restraints manager: 29.19 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: 13044 16.80 - 33.59: 663 33.59 - 50.39: 173 50.39 - 67.19: 111 67.19 - 83.99: 21 Dihedral angle restraints: 14012 sinusoidal: 6610 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 14009 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: 2.260 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: 0.520 Extract box with map and model: 11.140 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 117.410 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.920 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.111 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 outliers start: 10 outliers final: 7 residues processed: 286 average time/residue: 0.8274 time to fit residues: 331.8468 Evaluate side-chains 156 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4608 time to fit residues: 8.9773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 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: 3.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.1946 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= 0.259 Angle : 0.618 6.226 23947 Z= 0.323 Chirality : 0.041 0.167 2730 Planarity : 0.005 0.051 3086 Dihedral : 5.852 68.840 2368 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.93 % Allowed : 8.13 % Favored : 90.94 % 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: -1.58 (0.17), residues: 2181 helix: -0.40 (0.21), residues: 534 sheet: -1.27 (0.21), residues: 509 loop : -1.20 (0.18), residues: 1138 *********************** 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 175 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 3.015 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 outliers start: 18 outliers final: 15 residues processed: 168 average time/residue: 0.7817 time to fit residues: 191.9657 Evaluate side-chains 152 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4653 time to fit residues: 15.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 197 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17613 Z= 0.228 Angle : 0.570 7.905 23947 Z= 0.291 Chirality : 0.040 0.154 2730 Planarity : 0.004 0.053 3086 Dihedral : 5.406 66.791 2368 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.88 % Allowed : 8.64 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.18), residues: 2181 helix: 0.21 (0.23), residues: 534 sheet: -1.34 (0.22), residues: 503 loop : -0.94 (0.18), residues: 1144 *********************** 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 165 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 2.782 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 outliers start: 17 outliers final: 10 residues processed: 164 average time/residue: 0.7325 time to fit residues: 177.0064 Evaluate side-chains 138 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 3.522 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4071 time to fit residues: 10.8992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 94 optimal weight: 0.3980 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17613 Z= 0.165 Angle : 0.540 6.941 23947 Z= 0.274 Chirality : 0.039 0.145 2730 Planarity : 0.004 0.051 3086 Dihedral : 5.150 63.452 2368 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.47 % Allowed : 9.47 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2181 helix: 0.48 (0.23), residues: 535 sheet: -1.30 (0.22), residues: 500 loop : -0.81 (0.19), residues: 1146 *********************** 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 145 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 2.829 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 outliers start: 9 outliers final: 3 residues processed: 141 average time/residue: 0.8020 time to fit residues: 164.8970 Evaluate side-chains 130 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 2.754 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3702 time to fit residues: 5.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.7731 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17613 Z= 0.237 Angle : 0.543 6.259 23947 Z= 0.277 Chirality : 0.039 0.152 2730 Planarity : 0.004 0.051 3086 Dihedral : 5.052 65.307 2368 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.72 % Allowed : 9.52 % Favored : 89.75 % 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: 0.60 (0.23), residues: 536 sheet: -1.32 (0.22), residues: 501 loop : -0.80 (0.19), residues: 1144 *********************** 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 148 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 2.754 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 outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.7573 time to fit residues: 158.7991 Evaluate side-chains 129 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5594 time to fit residues: 10.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17613 Z= 0.210 Angle : 0.536 6.250 23947 Z= 0.272 Chirality : 0.039 0.180 2730 Planarity : 0.004 0.052 3086 Dihedral : 4.947 64.875 2368 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.36 % Allowed : 10.66 % Favored : 88.98 % 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: -0.88 (0.18), residues: 2181 helix: 0.68 (0.24), residues: 536 sheet: -1.36 (0.22), residues: 501 loop : -0.76 (0.19), residues: 1144 *********************** 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 131 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 3.530 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 outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.7618 time to fit residues: 145.4308 Evaluate side-chains 122 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 3.043 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4397 time to fit residues: 7.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 119 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7798 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17613 Z= 0.397 Angle : 0.596 6.346 23947 Z= 0.307 Chirality : 0.041 0.186 2730 Planarity : 0.004 0.055 3086 Dihedral : 5.142 69.423 2368 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.52 % Allowed : 11.18 % Favored : 88.30 % 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: 0.67 (0.23), residues: 530 sheet: -1.52 (0.22), residues: 494 loop : -0.95 (0.19), residues: 1157 *********************** 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 129 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 2.864 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 outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.7861 time to fit residues: 144.5116 Evaluate side-chains 117 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 2.825 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4099 time to fit residues: 8.1049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7745 moved from start: 0.3573 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= 0.197 Angle : 0.541 8.120 23947 Z= 0.273 Chirality : 0.040 0.202 2730 Planarity : 0.004 0.054 3086 Dihedral : 4.915 64.627 2368 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.26 % Allowed : 11.39 % Favored : 88.35 % 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: -0.92 (0.18), residues: 2181 helix: 0.82 (0.24), residues: 531 sheet: -1.46 (0.22), residues: 494 loop : -0.84 (0.19), residues: 1156 *********************** 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 119 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 2.527 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 outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 0.8177 time to fit residues: 142.7591 Evaluate side-chains 114 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 2.796 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4426 time to fit residues: 5.8683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 117 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17613 Z= 0.243 Angle : 0.546 7.817 23947 Z= 0.275 Chirality : 0.039 0.191 2730 Planarity : 0.004 0.054 3086 Dihedral : 4.885 65.767 2368 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.16 % Allowed : 11.70 % Favored : 88.15 % 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: 0.87 (0.24), residues: 531 sheet: -1.49 (0.22), residues: 505 loop : -0.84 (0.19), residues: 1145 *********************** 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 118 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 3.069 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 outliers start: 3 outliers final: 3 residues processed: 116 average time/residue: 0.7864 time to fit residues: 134.5701 Evaluate side-chains 113 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 2.721 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4426 time to fit residues: 5.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7795 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17613 Z= 0.320 Angle : 0.584 8.140 23947 Z= 0.296 Chirality : 0.040 0.223 2730 Planarity : 0.004 0.053 3086 Dihedral : 5.006 69.268 2368 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 12.06 % Favored : 87.84 % 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: -1.05 (0.18), residues: 2181 helix: 0.80 (0.24), residues: 531 sheet: -1.63 (0.22), residues: 500 loop : -0.91 (0.19), residues: 1150 ********************** 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 119 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 2.727 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 outliers start: 2 outliers final: 2 residues processed: 117 average time/residue: 0.7382 time to fit residues: 128.4666 Evaluate side-chains 116 residues out of total 1950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 2.575 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4565 time to fit residues: 4.9282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.165170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130323 restraints weight = 98420.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121634 restraints weight = 93716.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118676 restraints weight = 89605.493| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17613 Z= 0.192 Angle : 0.542 8.510 23947 Z= 0.269 Chirality : 0.039 0.197 2730 Planarity : 0.004 0.053 3086 Dihedral : 4.782 64.651 2368 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.10 % Allowed : 12.11 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2181 helix: 0.96 (0.24), residues: 534 sheet: -1.52 (0.22), residues: 507 loop : -0.83 (0.19), residues: 1140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5863.88 seconds wall clock time: 105 minutes 37.06 seconds (6337.06 seconds total)