Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:56:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cxm_30492/02_2023/7cxm_30492.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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 Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "F TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F GLU 540": "OE1" <-> "OE2" Residue "F GLU 551": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E GLU 540": "OE1" <-> "OE2" Residue "E GLU 551": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "L" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 74.344 69.270 125.166 1.00 62.19 S ATOM 2487 SG CYS A 306 73.435 69.560 128.822 1.00 58.05 S ATOM 2519 SG CYS A 310 77.097 69.366 127.772 1.00 55.23 S ATOM 3927 SG CYS A 487 60.685 78.628 112.105 1.00 67.79 S ATOM 5180 SG CYS A 645 59.239 78.664 115.620 1.00 71.75 S ATOM 5186 SG CYS A 646 61.947 76.085 114.637 1.00 70.24 S ATOM 12225 SG CYS F 26 49.898 78.666 63.761 1.00190.17 S ATOM 12246 SG CYS F 29 49.806 75.743 64.680 1.00194.08 S ATOM 12411 SG CYS F 50 36.912 78.108 85.770 1.00190.06 S ATOM 12441 SG CYS F 55 34.226 75.460 85.717 1.00192.87 S ATOM 12574 SG CYS F 72 33.195 79.003 85.469 1.00192.04 S ATOM 12148 SG CYS F 16 46.438 69.826 70.994 1.00196.13 S ATOM 12163 SG CYS F 19 48.064 66.790 69.330 1.00210.35 S ATOM 16696 SG CYS E 5 77.788 123.283 59.514 1.00115.67 S ATOM 16717 SG CYS E 8 79.050 126.656 60.728 1.00121.11 S ATOM 16855 SG CYS E 26 75.358 125.977 60.766 1.00117.77 S ATOM 16876 SG CYS E 29 76.994 126.341 57.462 1.00119.90 S ATOM 17041 SG CYS E 50 52.174 115.275 57.500 1.00136.65 S ATOM 17071 SG CYS E 55 50.637 114.350 54.299 1.00142.27 S ATOM 17204 SG CYS E 72 51.452 118.089 54.796 1.00142.05 S ATOM 16778 SG CYS E 16 71.088 117.748 52.291 1.00118.66 S ATOM 16793 SG CYS E 19 74.090 116.581 50.242 1.00123.83 S Time building chain proxies: 12.40, per 1000 atoms: 0.58 Number of scatterers: 21295 At special positions: 0 Unit cell: (145.14, 151.7, 186.96, 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 8 29.99 S 149 16.00 P 57 15.00 O 4175 8.00 N 3614 7.00 C 13292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 9.05 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 21 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 40.4% alpha, 12.2% beta 15 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.814A pdb=" N HIS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.720A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.795A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.539A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.649A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.722A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.707A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.787A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.502A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.533A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.357A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.957A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.181A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.804A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.874A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 791 removed outlier: 3.702A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.608A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.889A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 removed outlier: 3.808A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 917' Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.688A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.830A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 44 through 55 removed outlier: 4.528A pdb=" N GLU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 95 removed outlier: 3.660A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.586A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.775A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.582A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.819A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.089A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.755A pdb=" N LEU D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.383A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.863A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.037A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.544A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.659A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 removed outlier: 3.686A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 270 removed outlier: 5.445A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F 270 " --> pdb=" O VAL F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 289 through 299 removed outlier: 3.564A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.617A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.523A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 516 through 525 removed outlier: 4.266A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 557 through 567 removed outlier: 4.356A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 removed outlier: 3.675A pdb=" N ASP F 583 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 584 " --> pdb=" O LEU F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 580 through 584' Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.683A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.157A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 146 Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.622A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.507A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 515 through 523 Processing helix chain 'E' and resid 557 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.233A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.445A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 347 removed outlier: 3.840A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.801A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.582A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.669A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.669A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'F' and resid 14 through 15 removed outlier: 4.137A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.851A pdb=" N VAL F 154 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER F 166 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 277 through 281 removed outlier: 3.824A pdb=" N SER F 278 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR F 398 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS F 330 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N THR F 359 " --> pdb=" O CYS F 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 511 through 512 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.556A pdb=" N THR E 12 " --> pdb=" O GLY E 3 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.782A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'E' and resid 152 through 156 removed outlier: 7.202A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 163 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.223A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 530 through 532 removed outlier: 5.945A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ASP E 542 " --> pdb=" O VAL E 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 747 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 8.32 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3348 1.28 - 1.41: 5834 1.41 - 1.55: 12357 1.55 - 1.68: 117 1.68 - 1.82: 210 Bond restraints: 21866 Sorted by residual: bond pdb=" CA SER A 343 " pdb=" C SER A 343 " ideal model delta sigma weight residual 1.524 1.422 0.101 1.33e-02 5.65e+03 5.80e+01 bond pdb=" C PHE A 348 " pdb=" O PHE A 348 " ideal model delta sigma weight residual 1.234 1.145 0.089 1.22e-02 6.72e+03 5.33e+01 bond pdb=" C VAL A 342 " pdb=" O VAL A 342 " ideal model delta sigma weight residual 1.235 1.162 0.072 1.02e-02 9.61e+03 5.03e+01 bond pdb=" C TYR A 346 " pdb=" O TYR A 346 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.20e-02 6.94e+03 4.93e+01 bond pdb=" CA ASN D 109 " pdb=" C ASN D 109 " ideal model delta sigma weight residual 1.524 1.441 0.084 1.24e-02 6.50e+03 4.55e+01 ... (remaining 21861 not shown) Histogram of bond angle deviations from ideal: 74.01 - 87.95: 10 87.95 - 101.90: 224 101.90 - 115.85: 14159 115.85 - 129.79: 15439 129.79 - 143.74: 148 Bond angle restraints: 29980 Sorted by residual: angle pdb=" N ASP E 458 " pdb=" CA ASP E 458 " pdb=" C ASP E 458 " ideal model delta sigma weight residual 110.52 78.65 31.87 1.48e+00 4.57e-01 4.64e+02 angle pdb=" N SER F 36 " pdb=" CA SER F 36 " pdb=" C SER F 36 " ideal model delta sigma weight residual 114.31 140.70 -26.39 1.29e+00 6.01e-01 4.18e+02 angle pdb=" N CYS B 142 " pdb=" CA CYS B 142 " pdb=" C CYS B 142 " ideal model delta sigma weight residual 107.80 74.01 33.79 1.73e+00 3.34e-01 3.82e+02 angle pdb=" N THR A 344 " pdb=" CA THR A 344 " pdb=" C THR A 344 " ideal model delta sigma weight residual 109.96 79.88 30.08 1.58e+00 4.01e-01 3.63e+02 angle pdb=" N ALA D 126 " pdb=" CA ALA D 126 " pdb=" CB ALA D 126 " ideal model delta sigma weight residual 110.38 85.25 25.13 1.38e+00 5.25e-01 3.32e+02 ... (remaining 29975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 11805 25.53 - 51.06: 1008 51.06 - 76.59: 154 76.59 - 102.11: 14 102.11 - 127.64: 3 Dihedral angle restraints: 12984 sinusoidal: 5398 harmonic: 7586 Sorted by residual: dihedral pdb=" CA ALA A 17 " pdb=" C ALA A 17 " pdb=" N ARG A 18 " pdb=" CA ARG A 18 " ideal model delta harmonic sigma weight residual 180.00 54.72 125.28 0 5.00e+00 4.00e-02 6.28e+02 dihedral pdb=" C TRP B 182 " pdb=" N TRP B 182 " pdb=" CA TRP B 182 " pdb=" CB TRP B 182 " ideal model delta harmonic sigma weight residual -122.60 -157.01 34.41 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CA TRP B 182 " pdb=" CB TRP B 182 " ideal model delta harmonic sigma weight residual 122.80 156.80 -34.00 0 2.50e+00 1.60e-01 1.85e+02 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 3406 0.333 - 0.666: 46 0.666 - 0.999: 10 0.999 - 1.332: 1 1.332 - 1.665: 2 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.93e+01 chirality pdb=" CA PHE E 346 " pdb=" N PHE E 346 " pdb=" C PHE E 346 " pdb=" CB PHE E 346 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.64e+01 chirality pdb=" CA VAL A 257 " pdb=" N VAL A 257 " pdb=" C VAL A 257 " pdb=" CB VAL A 257 " both_signs ideal model delta sigma weight residual False 2.44 1.39 1.05 2.00e-01 2.50e+01 2.77e+01 ... (remaining 3462 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 460 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO A 461 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 183 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 115 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 116 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.060 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 43 2.24 - 2.90: 9450 2.90 - 3.57: 30266 3.57 - 4.23: 50635 4.23 - 4.90: 83125 Nonbonded interactions: 173519 Sorted by model distance: nonbonded pdb=" O SER D 177 " pdb=" CD2 LEU D 180 " model vdw 1.572 3.460 nonbonded pdb=" OD2 ASP A 260 " pdb=" NZ LYS A 263 " model vdw 1.709 2.520 nonbonded pdb=" SG CYS F 8 " pdb=" CG1 VAL F 98 " model vdw 1.795 3.820 nonbonded pdb=" O LEU A 900 " pdb=" O TYR A 903 " model vdw 1.819 3.040 nonbonded pdb=" CD2 HIS A 75 " pdb=" CG2 THR A 76 " model vdw 1.839 3.680 ... (remaining 173514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 596 or resid 701 through 703)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 596 or resid 1000 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 57 5.49 5 S 149 5.16 5 C 13292 2.51 5 N 3614 2.21 5 O 4175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 0.010 Extract box with map and model: 20.130 Check model and map are aligned: 0.360 Process input model: 65.390 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 0.010 0.112 21866 Z= 0.625 Angle : 1.585 33.794 29980 Z= 0.981 Chirality : 0.101 1.665 3465 Planarity : 0.006 0.118 3626 Dihedral : 18.068 127.642 8090 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.98 % Favored : 90.40 % Rotamer Outliers : 12.89 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.28 (0.13), residues: 2551 helix: -2.30 (0.14), residues: 944 sheet: -2.30 (0.26), residues: 301 loop : -3.47 (0.14), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 151 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 284 outliers final: 118 residues processed: 418 average time/residue: 1.0483 time to fit residues: 514.0525 Evaluate side-chains 244 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 126 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 116 residues processed: 2 average time/residue: 0.7963 time to fit residues: 5.2413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 752 HIS A 790 ASN A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN E 290 HIS E 311 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 21866 Z= 0.262 Angle : 0.780 21.512 29980 Z= 0.395 Chirality : 0.047 0.421 3465 Planarity : 0.005 0.066 3626 Dihedral : 7.930 125.968 3479 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % Rotamer Outliers : 10.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.15), residues: 2551 helix: -1.20 (0.16), residues: 949 sheet: -1.66 (0.28), residues: 300 loop : -2.98 (0.15), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 137 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 116 residues processed: 351 average time/residue: 1.0247 time to fit residues: 425.3207 Evaluate side-chains 240 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 124 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 112 residues processed: 4 average time/residue: 0.6004 time to fit residues: 5.8742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 233 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 231 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 108 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 21866 Z= 0.364 Angle : 0.748 20.826 29980 Z= 0.379 Chirality : 0.047 0.301 3465 Planarity : 0.004 0.073 3626 Dihedral : 7.679 128.426 3479 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.21 % Favored : 90.63 % Rotamer Outliers : 10.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.15), residues: 2551 helix: -0.90 (0.17), residues: 968 sheet: -1.51 (0.28), residues: 296 loop : -2.71 (0.15), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 121 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 224 outliers final: 134 residues processed: 329 average time/residue: 0.9804 time to fit residues: 384.8417 Evaluate side-chains 253 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 119 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 130 residues processed: 4 average time/residue: 0.4856 time to fit residues: 6.0829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 234 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 886 GLN A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN E 388 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21866 Z= 0.216 Angle : 0.678 20.685 29980 Z= 0.338 Chirality : 0.043 0.244 3465 Planarity : 0.004 0.051 3626 Dihedral : 7.273 126.909 3479 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.53 % Favored : 92.32 % Rotamer Outliers : 9.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.29 (0.16), residues: 2551 helix: -0.50 (0.17), residues: 962 sheet: -1.26 (0.29), residues: 286 loop : -2.43 (0.16), residues: 1303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 134 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 203 outliers final: 135 residues processed: 324 average time/residue: 0.9776 time to fit residues: 379.4765 Evaluate side-chains 263 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 128 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 132 residues processed: 3 average time/residue: 0.2481 time to fit residues: 4.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 0.2980 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21866 Z= 0.170 Angle : 0.653 20.781 29980 Z= 0.323 Chirality : 0.042 0.227 3465 Planarity : 0.004 0.050 3626 Dihedral : 6.969 126.458 3479 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.25 % Favored : 92.59 % Rotamer Outliers : 8.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.98 (0.16), residues: 2551 helix: -0.27 (0.17), residues: 961 sheet: -1.07 (0.29), residues: 293 loop : -2.24 (0.16), residues: 1297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 133 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 124 residues processed: 303 average time/residue: 1.0878 time to fit residues: 388.0989 Evaluate side-chains 248 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 124 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 121 residues processed: 3 average time/residue: 0.6266 time to fit residues: 5.8222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 145 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 206 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 209 ASN A 492 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN E 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 21866 Z= 0.150 Angle : 0.642 20.802 29980 Z= 0.314 Chirality : 0.041 0.231 3465 Planarity : 0.004 0.072 3626 Dihedral : 6.695 125.342 3479 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.74 % Favored : 93.10 % Rotamer Outliers : 7.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2551 helix: 0.00 (0.18), residues: 959 sheet: -0.91 (0.29), residues: 304 loop : -2.01 (0.17), residues: 1288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 131 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 102 residues processed: 285 average time/residue: 1.0996 time to fit residues: 373.7013 Evaluate side-chains 226 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 124 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 102 residues processed: 0 time to fit residues: 3.0288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 140 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 492 GLN A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN F 537 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 21866 Z= 0.308 Angle : 0.690 20.630 29980 Z= 0.342 Chirality : 0.044 0.270 3465 Planarity : 0.004 0.047 3626 Dihedral : 6.802 126.763 3479 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.84 % Favored : 92.04 % Rotamer Outliers : 6.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2551 helix: -0.11 (0.17), residues: 960 sheet: -0.99 (0.29), residues: 301 loop : -2.03 (0.17), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 128 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 106 residues processed: 271 average time/residue: 1.0902 time to fit residues: 348.0381 Evaluate side-chains 231 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 125 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 104 residues processed: 2 average time/residue: 0.7864 time to fit residues: 5.3127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21866 Z= 0.172 Angle : 0.646 20.763 29980 Z= 0.317 Chirality : 0.041 0.218 3465 Planarity : 0.004 0.048 3626 Dihedral : 6.655 124.672 3479 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.13 % Favored : 92.71 % Rotamer Outliers : 5.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2551 helix: 0.09 (0.18), residues: 960 sheet: -0.84 (0.29), residues: 299 loop : -1.95 (0.17), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 133 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 103 residues processed: 253 average time/residue: 1.2228 time to fit residues: 368.4334 Evaluate side-chains 226 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 123 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 102 residues processed: 1 average time/residue: 0.2079 time to fit residues: 3.6759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 909 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 21866 Z= 0.334 Angle : 0.702 20.631 29980 Z= 0.349 Chirality : 0.045 0.276 3465 Planarity : 0.004 0.048 3626 Dihedral : 6.776 125.863 3479 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.23 % Favored : 91.65 % Rotamer Outliers : 5.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2551 helix: -0.05 (0.17), residues: 962 sheet: -0.96 (0.29), residues: 300 loop : -1.97 (0.17), residues: 1289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 128 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 102 residues processed: 249 average time/residue: 1.1219 time to fit residues: 329.7648 Evaluate side-chains 227 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 125 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 102 residues processed: 0 time to fit residues: 3.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 21866 Z= 0.229 Angle : 0.679 20.713 29980 Z= 0.333 Chirality : 0.043 0.241 3465 Planarity : 0.004 0.048 3626 Dihedral : 6.698 124.147 3479 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.45 % Favored : 92.43 % Rotamer Outliers : 5.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2551 helix: 0.05 (0.17), residues: 963 sheet: -0.92 (0.29), residues: 300 loop : -1.90 (0.17), residues: 1288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 125 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 103 residues processed: 237 average time/residue: 1.1211 time to fit residues: 313.2689 Evaluate side-chains 223 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 120 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 103 residues processed: 0 time to fit residues: 3.2540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 209 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 179 optimal weight: 8.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.131037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072016 restraints weight = 47560.481| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.92 r_work: 0.3009 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21866 Z= 0.166 Angle : 0.655 20.712 29980 Z= 0.319 Chirality : 0.041 0.323 3465 Planarity : 0.004 0.047 3626 Dihedral : 6.508 122.749 3479 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.45 % Favored : 92.43 % Rotamer Outliers : 5.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % 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: -1.28 (0.17), residues: 2551 helix: 0.26 (0.18), residues: 958 sheet: -0.71 (0.29), residues: 300 loop : -1.77 (0.17), residues: 1293 =============================================================================== Job complete usr+sys time: 7797.49 seconds wall clock time: 139 minutes 44.06 seconds (8384.06 seconds total)