Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:17:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ify_9658/02_2023/6ify_9658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ify_9658/02_2023/6ify_9658.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/6ify_9658/02_2023/6ify_9658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ify_9658/02_2023/6ify_9658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ify_9658/02_2023/6ify_9658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ify_9658/02_2023/6ify_9658.pdb" } resolution = 3.8 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= 0.013 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 GLU 4": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H ARG 158": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19085 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5733 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 8, 'TRANS': 724} Chain breaks: 3 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 989 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1694 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1593 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2292 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2772 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Chain: "A" 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 2846 SG CYS A 401 57.843 30.797 65.672 1.00 62.78 S ATOM 2869 SG CYS A 404 55.290 32.198 63.265 1.00 63.76 S ATOM 3013 SG CYS A 422 58.505 33.792 63.733 1.00 60.33 S Time building chain proxies: 11.12, per 1000 atoms: 0.58 Number of scatterers: 19085 At special positions: 0 Unit cell: (91.52, 134.16, 171.6, 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 1 29.99 S 37 16.00 P 62 15.00 O 3782 8.00 N 3241 7.00 C 11962 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: 8.02 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4252 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 21 sheets defined 38.5% alpha, 10.7% beta 22 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.606A pdb=" N ILE A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.769A pdb=" N VAL A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 removed outlier: 4.191A pdb=" N VAL A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.553A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.633A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.598A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.410A pdb=" N ASP A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 228' Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.466A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.923A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 removed outlier: 4.041A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 removed outlier: 3.751A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.858A pdb=" N ASP A 415 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.758A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.719A pdb=" N ASN A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 498 " --> pdb=" O ILE A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.559A pdb=" N GLN A 533 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.065A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.285A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.644A pdb=" N HIS A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 removed outlier: 4.326A pdb=" N THR A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.837A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.952A pdb=" N MET A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 3.583A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 37 through 57 removed outlier: 4.117A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.891A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 4.603A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.514A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.857A pdb=" N ASN C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 removed outlier: 4.168A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.621A pdb=" N LYS C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.561A pdb=" N TYR C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 65 removed outlier: 3.694A pdb=" N LEU G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 removed outlier: 3.623A pdb=" N SER G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 166 removed outlier: 3.661A pdb=" N ASP G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 Processing helix chain 'G' and resid 176 through 180 Processing helix chain 'F' and resid 48 through 65 removed outlier: 3.581A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 65 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.670A pdb=" N ASP F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.602A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.507A pdb=" N ARG F 188 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 removed outlier: 3.687A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 84 Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.323A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.714A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 removed outlier: 4.241A pdb=" N ASN E 161 " --> pdb=" O GLU E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.531A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.738A pdb=" N ARG E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 208 through 211 removed outlier: 4.155A pdb=" N THR E 211 " --> pdb=" O ASP E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.633A pdb=" N PHE B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.585A pdb=" N PHE B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.696A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 removed outlier: 3.617A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.503A pdb=" N ASP B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.885A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.677A pdb=" N LEU H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 148 removed outlier: 3.586A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 184 Processing helix chain 'H' and resid 236 through 245 Processing helix chain 'H' and resid 245 through 261 removed outlier: 4.862A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 289 Processing sheet with id=AA1, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.990A pdb=" N ALA A 244 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.667A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 575 removed outlier: 6.750A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 574 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 579 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 96 through 97 removed outlier: 6.608A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 146 through 149 removed outlier: 3.746A pdb=" N LYS G 192 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 122 removed outlier: 3.605A pdb=" N ARG G 140 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS G 121 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 146 through 155 removed outlier: 7.090A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.505A pdb=" N LYS E 7 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.659A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 7 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 133 removed outlier: 3.509A pdb=" N LYS B 133 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 143 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'H' and resid 185 through 186 removed outlier: 3.733A pdb=" N THR H 233 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'H' and resid 32 through 33 removed outlier: 3.512A pdb=" N PHE H 40 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 214 through 219 removed outlier: 4.550A pdb=" N LYS H 202 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU H 217 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL H 200 " --> pdb=" O LEU H 217 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4064 1.33 - 1.45: 4727 1.45 - 1.57: 10594 1.57 - 1.69: 122 1.69 - 1.81: 66 Bond restraints: 19573 Sorted by residual: bond pdb=" CG ASP A 67 " pdb=" OD2 ASP A 67 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.67e+01 bond pdb=" N LYS H 313 " pdb=" CA LYS H 313 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.68e+00 bond pdb=" N VAL H 315 " pdb=" CA VAL H 315 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.19e+00 bond pdb=" N VAL H 311 " pdb=" CA VAL H 311 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 bond pdb=" C SER A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.30e-02 5.92e+03 7.35e+00 ... (remaining 19568 not shown) Histogram of bond angle deviations from ideal: 98.37 - 106.28: 656 106.28 - 114.20: 11160 114.20 - 122.12: 11129 122.12 - 130.03: 3671 130.03 - 137.95: 91 Bond angle restraints: 26707 Sorted by residual: angle pdb=" C LYS A 133 " pdb=" N PRO A 134 " pdb=" CA PRO A 134 " ideal model delta sigma weight residual 119.84 137.95 -18.11 1.25e+00 6.40e-01 2.10e+02 angle pdb=" C TYR B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta sigma weight residual 119.90 107.85 12.05 1.05e+00 9.07e-01 1.32e+02 angle pdb=" N PRO B 79 " pdb=" CA PRO B 79 " pdb=" C PRO B 79 " ideal model delta sigma weight residual 110.80 98.58 12.22 1.51e+00 4.39e-01 6.55e+01 angle pdb=" C ALA B 29 " pdb=" CA ALA B 29 " pdb=" CB ALA B 29 " ideal model delta sigma weight residual 111.23 99.54 11.69 1.63e+00 3.76e-01 5.14e+01 angle pdb=" N LYS A 133 " pdb=" CA LYS A 133 " pdb=" C LYS A 133 " ideal model delta sigma weight residual 108.45 121.60 -13.15 1.93e+00 2.68e-01 4.64e+01 ... (remaining 26702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 11301 35.40 - 70.80: 297 70.80 - 106.19: 15 106.19 - 141.59: 1 141.59 - 176.99: 2 Dihedral angle restraints: 11616 sinusoidal: 5025 harmonic: 6591 Sorted by residual: dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 48.99 -176.99 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 14 " pdb=" C1' C I 14 " pdb=" N1 C I 14 " pdb=" C2 C I 14 " ideal model delta sinusoidal sigma weight residual -128.00 4.64 -132.64 1 1.70e+01 3.46e-03 5.57e+01 dihedral pdb=" CA ILE H 20 " pdb=" C ILE H 20 " pdb=" N GLY H 21 " pdb=" CA GLY H 21 " ideal model delta harmonic sigma weight residual 180.00 143.88 36.12 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2971 0.160 - 0.321: 46 0.321 - 0.481: 4 0.481 - 0.641: 0 0.641 - 0.802: 1 Chirality restraints: 3022 Sorted by residual: chirality pdb=" CA TYR B 78 " pdb=" N TYR B 78 " pdb=" C TYR B 78 " pdb=" CB TYR B 78 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA LYS A 133 " pdb=" N LYS A 133 " pdb=" C LYS A 133 " pdb=" CB LYS A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 3019 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 638 " 0.026 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C GLY A 638 " -0.093 2.00e-02 2.50e+03 pdb=" O GLY A 638 " 0.035 2.00e-02 2.50e+03 pdb=" N ASN A 639 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.041 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" N9 G I 21 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 21 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.040 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 A I 27 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A I 27 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A I 27 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.001 2.00e-02 2.50e+03 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 59 2.37 - 3.00: 9650 3.00 - 3.63: 29658 3.63 - 4.27: 46529 4.27 - 4.90: 75103 Nonbonded interactions: 160999 Sorted by model distance: nonbonded pdb=" CD2 TYR H 33 " pdb=" O ALA H 108 " model vdw 1.733 3.340 nonbonded pdb=" CE2 TYR H 33 " pdb=" O ALA H 108 " model vdw 1.763 3.340 nonbonded pdb=" ND2 ASN A 639 " pdb=" OG SER A 643 " model vdw 1.812 2.520 nonbonded pdb=" OE2 GLU A 192 " pdb=" OE1 GLN A 538 " model vdw 2.016 3.040 nonbonded pdb=" OG1 THR C 5 " pdb=" OD1 ASN C 8 " model vdw 2.039 2.440 ... (remaining 160994 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 'C' and (resid 3 through 101 or (resid 102 and (name N or name CA or name \ C or name O or name CB )) or resid 103 through 123)) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 217)) selection = (chain 'F' and (resid 2 through 25 or (resid 26 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 65 or resid 76 through 1 \ 31 or (resid 132 through 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 156 or (resid 157 through 158 and (na \ me N or name CA or name C or name O or name CB )) or resid 159 or (resid 160 thr \ ough 161 and (name N or name CA or name C or name O or name CB )) or resid 162 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 25 or (resid 26 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 65 or resid 76 through 1 \ 06 or (resid 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 131 or (resid 132 through 133 and (name N or name CA or name C or \ name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or name \ CA or name C or name O or name CB )) or resid 138 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 217)) \ } 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 1 6.06 5 P 62 5.49 5 S 37 5.16 5 C 11962 2.51 5 N 3241 2.21 5 O 3782 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 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.740 Check model and map are aligned: 0.300 Process input model: 54.650 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.005 0.082 19573 Z= 0.332 Angle : 1.031 18.106 26707 Z= 0.585 Chirality : 0.060 0.802 3022 Planarity : 0.006 0.065 3214 Dihedral : 15.924 176.990 7364 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.74 % Favored : 88.99 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.14 (0.13), residues: 2225 helix: -3.34 (0.12), residues: 776 sheet: -3.29 (0.23), residues: 363 loop : -3.49 (0.15), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 535 time to evaluate : 2.257 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 outliers start: 15 outliers final: 6 residues processed: 547 average time/residue: 0.3557 time to fit residues: 283.5764 Evaluate side-chains 306 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 300 time to evaluate : 2.131 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2465 time to fit residues: 5.3089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 0.0020 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 167 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN A 409 ASN A 414 HIS A 561 ASN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN D 76 GLN C 26 ASN G 85 ASN G 137 GLN F 33 ASN F 197 ASN E 85 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN B 14 HIS B 125 HIS B 233 HIS B 273 GLN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 19573 Z= 0.246 Angle : 0.722 12.906 26707 Z= 0.379 Chirality : 0.047 0.375 3022 Planarity : 0.004 0.048 3214 Dihedral : 11.792 173.895 3189 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.16 % Favored : 89.75 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.20 (0.15), residues: 2225 helix: -2.25 (0.15), residues: 819 sheet: -2.95 (0.25), residues: 340 loop : -3.16 (0.16), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 340 time to evaluate : 2.275 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 outliers start: 55 outliers final: 30 residues processed: 372 average time/residue: 0.3147 time to fit residues: 178.8544 Evaluate side-chains 308 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 278 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1964 time to fit residues: 13.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 204 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 661 ASN A 677 GLN A 727 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 19573 Z= 0.275 Angle : 0.705 12.969 26707 Z= 0.371 Chirality : 0.046 0.341 3022 Planarity : 0.004 0.045 3214 Dihedral : 11.705 179.116 3189 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.83 % Favored : 89.12 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.16), residues: 2225 helix: -1.74 (0.16), residues: 818 sheet: -2.94 (0.25), residues: 343 loop : -2.97 (0.17), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 300 time to evaluate : 1.974 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 outliers start: 45 outliers final: 21 residues processed: 334 average time/residue: 0.3050 time to fit residues: 157.3778 Evaluate side-chains 280 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1888 time to fit residues: 10.3820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.0270 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 497 ASN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 19573 Z= 0.238 Angle : 0.678 11.265 26707 Z= 0.353 Chirality : 0.045 0.343 3022 Planarity : 0.004 0.040 3214 Dihedral : 11.584 178.806 3189 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.56 % Favored : 89.39 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2225 helix: -1.35 (0.17), residues: 821 sheet: -2.72 (0.26), residues: 338 loop : -2.83 (0.17), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 289 time to evaluate : 2.442 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 outliers start: 45 outliers final: 28 residues processed: 313 average time/residue: 0.3211 time to fit residues: 155.2148 Evaluate side-chains 285 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1976 time to fit residues: 12.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 19573 Z= 0.367 Angle : 0.755 11.215 26707 Z= 0.394 Chirality : 0.047 0.366 3022 Planarity : 0.004 0.049 3214 Dihedral : 11.876 179.353 3189 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.85 % Favored : 87.10 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.41 (0.16), residues: 2225 helix: -1.32 (0.17), residues: 817 sheet: -2.76 (0.25), residues: 347 loop : -2.85 (0.18), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 267 time to evaluate : 2.194 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 outliers start: 51 outliers final: 22 residues processed: 303 average time/residue: 0.3157 time to fit residues: 149.1048 Evaluate side-chains 261 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1974 time to fit residues: 11.2106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS B 249 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 19573 Z= 0.235 Angle : 0.685 11.357 26707 Z= 0.356 Chirality : 0.045 0.358 3022 Planarity : 0.004 0.048 3214 Dihedral : 11.636 179.554 3189 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.29 % Favored : 89.66 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.21 (0.17), residues: 2225 helix: -1.10 (0.17), residues: 834 sheet: -2.53 (0.26), residues: 333 loop : -2.86 (0.18), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 2.385 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 outliers start: 40 outliers final: 15 residues processed: 304 average time/residue: 0.3132 time to fit residues: 146.5499 Evaluate side-chains 259 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1767 time to fit residues: 7.7441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 0.0070 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 19573 Z= 0.204 Angle : 0.672 11.602 26707 Z= 0.345 Chirality : 0.044 0.335 3022 Planarity : 0.004 0.044 3214 Dihedral : 11.457 179.049 3189 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.38 % Favored : 89.57 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.01 (0.17), residues: 2225 helix: -0.86 (0.17), residues: 834 sheet: -2.46 (0.27), residues: 333 loop : -2.80 (0.18), residues: 1058 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 280 time to evaluate : 2.051 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 outliers start: 25 outliers final: 12 residues processed: 294 average time/residue: 0.3075 time to fit residues: 139.9666 Evaluate side-chains 265 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1826 time to fit residues: 6.8333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 10.0000 chunk 87 optimal weight: 0.0770 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 overall best weight: 6.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 19573 Z= 0.354 Angle : 0.760 13.334 26707 Z= 0.394 Chirality : 0.047 0.355 3022 Planarity : 0.004 0.061 3214 Dihedral : 11.710 179.437 3189 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.27 % Favored : 87.64 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.17), residues: 2225 helix: -1.03 (0.17), residues: 831 sheet: -2.47 (0.27), residues: 333 loop : -2.87 (0.18), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 13 residues processed: 272 average time/residue: 0.3163 time to fit residues: 133.7708 Evaluate side-chains 253 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 240 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1939 time to fit residues: 7.5238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 203 optimal weight: 0.5980 chunk 122 optimal weight: 0.0270 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 81 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 19573 Z= 0.218 Angle : 0.711 11.949 26707 Z= 0.366 Chirality : 0.045 0.342 3022 Planarity : 0.004 0.048 3214 Dihedral : 11.500 178.657 3189 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.80 % Favored : 90.11 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.17), residues: 2225 helix: -0.86 (0.17), residues: 832 sheet: -2.39 (0.27), residues: 333 loop : -2.79 (0.18), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 274 time to evaluate : 2.097 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 outliers start: 23 outliers final: 8 residues processed: 288 average time/residue: 0.3131 time to fit residues: 141.1886 Evaluate side-chains 256 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 248 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1881 time to fit residues: 5.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 19573 Z= 0.295 Angle : 0.749 13.766 26707 Z= 0.387 Chirality : 0.046 0.340 3022 Planarity : 0.004 0.043 3214 Dihedral : 11.551 179.580 3189 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.60 % Favored : 88.31 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.03 (0.17), residues: 2225 helix: -0.89 (0.17), residues: 832 sheet: -2.41 (0.27), residues: 333 loop : -2.83 (0.18), residues: 1060 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 2.146 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 outliers start: 18 outliers final: 9 residues processed: 264 average time/residue: 0.3284 time to fit residues: 136.5232 Evaluate side-chains 253 residues out of total 1949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2005 time to fit residues: 6.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 75 optimal weight: 0.0770 chunk 185 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.114887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103174 restraints weight = 55211.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105141 restraints weight = 31454.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106422 restraints weight = 20900.627| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19573 Z= 0.214 Angle : 0.710 13.420 26707 Z= 0.366 Chirality : 0.044 0.326 3022 Planarity : 0.004 0.046 3214 Dihedral : 11.390 178.101 3189 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.89 % Favored : 90.02 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.91 (0.17), residues: 2225 helix: -0.83 (0.17), residues: 849 sheet: -2.24 (0.27), residues: 336 loop : -2.79 (0.18), residues: 1040 =============================================================================== Job complete usr+sys time: 3591.49 seconds wall clock time: 66 minutes 32.02 seconds (3992.02 seconds total)