Starting phenix.real_space_refine on Mon Dec 11 08:09:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mut_9255/12_2023/6mut_9255_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 38 5.49 5 S 50 5.16 5 C 10800 2.51 5 N 2991 2.21 5 O 3269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17151 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5958 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 713} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1143 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2202 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2138 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 440 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna2p': 9, 'rna3p': 10} Chain: "H" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "F" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2618 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 10, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 250 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3111 SG CYS A 389 47.005 69.717 95.875 1.00 49.83 S ATOM 3131 SG CYS A 392 45.001 66.558 95.210 1.00 47.28 S ATOM 3286 SG CYS A 413 45.413 68.202 98.783 1.00 48.96 S ATOM 3306 SG CYS A 416 47.913 65.828 97.907 1.00 46.14 S ATOM 7916 SG CYS C 113 55.739 95.945 78.587 1.00 47.08 S ATOM 7983 SG CYS C 122 57.365 96.835 75.093 1.00 42.26 S ATOM 8003 SG CYS C 125 55.610 92.889 76.569 1.00 36.60 S ATOM 10134 SG CYS D 113 86.479 81.027 78.348 1.00 64.42 S ATOM 10201 SG CYS D 122 88.282 82.794 75.313 1.00 61.95 S ATOM 10221 SG CYS D 125 85.158 80.035 74.681 1.00 56.51 S Time building chain proxies: 9.71, per 1000 atoms: 0.57 Number of scatterers: 17151 At special positions: 0 Unit cell: (137.214, 118.701, 142.659, 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 3 29.99 S 50 16.00 P 38 15.00 O 3269 8.00 N 2991 7.00 C 10800 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: 6.73 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 38.3% alpha, 13.5% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.755A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.870A pdb=" N ARG A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 removed outlier: 5.060A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.563A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.529A pdb=" N VAL A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 171 through 183 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.627A pdb=" N LEU A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.634A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.857A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.974A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.847A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.641A pdb=" N SER A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.784A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.712A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 removed outlier: 3.640A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.635A pdb=" N ALA A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.641A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 717 removed outlier: 3.750A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.751A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.681A pdb=" N VAL A 746 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.503A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 4.039A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.548A pdb=" N ASP B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.777A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 removed outlier: 4.390A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.561A pdb=" N GLU B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.939A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.563A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 4.220A pdb=" N GLN B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.820A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.615A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.715A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 3.587A pdb=" N ALA D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.539A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.761A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.515A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.601A pdb=" N LEU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.530A pdb=" N PHE E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.674A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 removed outlier: 4.530A pdb=" N ALA E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 99 removed outlier: 4.014A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.596A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.614A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 3.955A pdb=" N GLY E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 51 through 60 removed outlier: 4.014A pdb=" N LEU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.547A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.703A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.690A pdb=" N ARG F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.483A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.560A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.538A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 304 removed outlier: 3.953A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 326 removed outlier: 3.749A pdb=" N SER F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 326 " --> pdb=" O TYR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.951A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 3.559A pdb=" N ASN F 359 " --> pdb=" O TYR F 355 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 292 removed outlier: 5.946A pdb=" N VAL A 288 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 299 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 290 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 295 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.906A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.798A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA A 585 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.986A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 15 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS C 8 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE C 245 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 259 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.888A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB1, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.886A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.083A pdb=" N SER D 242 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS D 14 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE D 240 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS D 16 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE D 238 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 163 through 167 removed outlier: 3.533A pdb=" N LYS D 166 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.659A pdb=" N THR E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU E 160 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA E 57 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR E 158 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY E 156 " --> pdb=" O PRO E 59 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.552A pdb=" N VAL E 133 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB8, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AB9, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC1, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC2, first strand: chain 'F' and resid 250 through 251 removed outlier: 3.652A pdb=" N VAL F 251 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.602A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AC5, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3400 1.32 - 1.45: 4540 1.45 - 1.57: 9496 1.57 - 1.69: 73 1.69 - 1.82: 82 Bond restraints: 17591 Sorted by residual: bond pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta sigma weight residual 1.444 1.483 -0.038 9.60e-03 1.09e+04 1.58e+01 bond pdb=" N ILE A 195 " pdb=" CA ILE A 195 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.46e+01 bond pdb=" N ARG A 117 " pdb=" CA ARG A 117 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N GLY F 365 " pdb=" CA GLY F 365 " ideal model delta sigma weight residual 1.447 1.486 -0.040 1.09e-02 8.42e+03 1.32e+01 bond pdb=" N VAL E 127 " pdb=" CA VAL E 127 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.06e+01 ... (remaining 17586 not shown) Histogram of bond angle deviations from ideal: 95.14 - 102.96: 173 102.96 - 110.77: 5925 110.77 - 118.59: 7905 118.59 - 126.41: 9617 126.41 - 134.22: 338 Bond angle restraints: 23958 Sorted by residual: angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 102.65 110.00 -7.35 6.80e-01 2.16e+00 1.17e+02 angle pdb=" C ASN C 179 " pdb=" N PRO C 180 " pdb=" CA PRO C 180 " ideal model delta sigma weight residual 119.85 129.71 -9.86 1.01e+00 9.80e-01 9.53e+01 angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.18 -7.10 9.70e-01 1.06e+00 5.36e+01 angle pdb=" C LEU E 219 " pdb=" N PRO E 220 " pdb=" CA PRO E 220 " ideal model delta sigma weight residual 119.76 127.26 -7.50 1.03e+00 9.43e-01 5.30e+01 angle pdb=" N PRO F 79 " pdb=" CA PRO F 79 " pdb=" CB PRO F 79 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.19e+01 ... (remaining 23953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 10299 33.87 - 67.74: 202 67.74 - 101.61: 23 101.61 - 135.48: 1 135.48 - 169.35: 2 Dihedral angle restraints: 10527 sinusoidal: 4495 harmonic: 6032 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 41.35 -169.35 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C G 20 " pdb=" C1' C G 20 " pdb=" N1 C G 20 " pdb=" C2 C G 20 " ideal model delta sinusoidal sigma weight residual 232.00 69.54 162.46 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" C5' C G 20 " pdb=" C4' C G 20 " pdb=" C3' C G 20 " pdb=" O3' C G 20 " ideal model delta sinusoidal sigma weight residual 147.00 107.36 39.64 1 8.00e+00 1.56e-02 3.45e+01 ... (remaining 10524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2168 0.098 - 0.195: 399 0.195 - 0.293: 71 0.293 - 0.390: 5 0.390 - 0.488: 1 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL E 157 " pdb=" CA VAL E 157 " pdb=" CG1 VAL E 157 " pdb=" CG2 VAL E 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' G G 16 " pdb=" C3' G G 16 " pdb=" O2' G G 16 " pdb=" C1' G G 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 2641 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 229 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C LEU E 229 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU E 229 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU E 230 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 89 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C CYS C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O CYS C 89 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 192 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ALA E 192 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA E 192 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY E 193 " 0.020 2.00e-02 2.50e+03 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 56 2.44 - 3.06: 10063 3.06 - 3.67: 25484 3.67 - 4.29: 38693 4.29 - 4.90: 64526 Nonbonded interactions: 138822 Sorted by model distance: nonbonded pdb=" O2' G G 16 " pdb=" O5' A G 17 " model vdw 1.830 2.440 nonbonded pdb=" O6 G G 16 " pdb=" O4 U H 29 " model vdw 1.969 2.432 nonbonded pdb=" O ASN A 102 " pdb=" CA GLY A 106 " model vdw 2.004 3.440 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.191 3.040 nonbonded pdb=" O2' G G 16 " pdb=" C8 A G 17 " model vdw 2.202 3.260 ... (remaining 138817 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 168 or resid 180 through 287 or resid 301)) selection = (chain 'D' and (resid 3 through 287 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.000 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: 4.360 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.400 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 0.013 0.142 17591 Z= 0.838 Angle : 1.286 10.922 23958 Z= 0.785 Chirality : 0.079 0.488 2644 Planarity : 0.009 0.076 2951 Dihedral : 14.102 169.354 6667 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.48 % Favored : 92.32 % Rotamer: Outliers : 1.23 % Allowed : 6.07 % Favored : 92.71 % Cbeta Deviations : 0.10 % 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: -4.80 (0.15), residues: 2071 helix: -4.17 (0.10), residues: 779 sheet: -1.54 (0.29), residues: 298 loop : -2.81 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP E 227 HIS 0.017 0.003 HIS A 382 PHE 0.038 0.004 PHE A 343 TYR 0.042 0.004 TYR D 49 ARG 0.018 0.002 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 319 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 333 average time/residue: 0.3893 time to fit residues: 178.7644 Evaluate side-chains 199 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1932 time to fit residues: 6.9210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 50.0000 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 191 optimal weight: 30.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 83 ASN C 179 ASN D 136 ASN D 199 ASN E 106 ASN E 200 HIS E 217 ASN F 18 ASN F 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17591 Z= 0.185 Angle : 0.630 8.645 23958 Z= 0.329 Chirality : 0.044 0.167 2644 Planarity : 0.006 0.054 2951 Dihedral : 14.120 173.806 2906 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.21 % Allowed : 10.05 % Favored : 87.75 % 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: -3.62 (0.16), residues: 2071 helix: -2.66 (0.14), residues: 809 sheet: -1.29 (0.30), residues: 266 loop : -2.43 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.004 0.001 HIS A 14 PHE 0.015 0.001 PHE D 243 TYR 0.017 0.001 TYR A 265 ARG 0.006 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 243 average time/residue: 0.3558 time to fit residues: 124.3584 Evaluate side-chains 197 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1587 time to fit residues: 7.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 0.0370 chunk 59 optimal weight: 0.1980 chunk 159 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 0.0570 chunk 191 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 177 GLN D 199 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17591 Z= 0.146 Angle : 0.546 8.554 23958 Z= 0.281 Chirality : 0.042 0.193 2644 Planarity : 0.004 0.044 2951 Dihedral : 13.818 175.130 2906 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 11.34 % Favored : 86.64 % 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: -2.80 (0.16), residues: 2071 helix: -1.70 (0.16), residues: 821 sheet: -1.26 (0.28), residues: 280 loop : -2.12 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 596 HIS 0.004 0.001 HIS D 111 PHE 0.010 0.001 PHE E 159 TYR 0.013 0.001 TYR A 490 ARG 0.017 0.000 ARG F 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 220 average time/residue: 0.3456 time to fit residues: 111.6188 Evaluate side-chains 184 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1958 time to fit residues: 6.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 203 optimal weight: 50.0000 chunk 100 optimal weight: 0.8980 chunk 182 optimal weight: 40.0000 chunk 54 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 92 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17591 Z= 0.192 Angle : 0.546 10.364 23958 Z= 0.278 Chirality : 0.043 0.204 2644 Planarity : 0.004 0.041 2951 Dihedral : 13.736 176.239 2906 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.39 % Allowed : 12.75 % Favored : 84.87 % 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: -2.30 (0.17), residues: 2071 helix: -1.16 (0.17), residues: 814 sheet: -1.13 (0.28), residues: 277 loop : -1.90 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS D 205 PHE 0.024 0.001 PHE A 491 TYR 0.019 0.001 TYR A 265 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.925 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 15 residues processed: 206 average time/residue: 0.3394 time to fit residues: 102.8838 Evaluate side-chains 180 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1577 time to fit residues: 7.1525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 174 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 51 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17591 Z= 0.238 Angle : 0.557 9.809 23958 Z= 0.283 Chirality : 0.043 0.191 2644 Planarity : 0.004 0.039 2951 Dihedral : 13.710 177.574 2906 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.65 % Allowed : 13.66 % Favored : 84.68 % 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: -2.01 (0.17), residues: 2071 helix: -0.86 (0.18), residues: 822 sheet: -0.98 (0.28), residues: 287 loop : -1.82 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 227 HIS 0.004 0.001 HIS D 205 PHE 0.016 0.001 PHE A 491 TYR 0.019 0.001 TYR A 265 ARG 0.005 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 198 average time/residue: 0.3408 time to fit residues: 100.6862 Evaluate side-chains 183 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1994 time to fit residues: 7.3032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 8.9990 chunk 183 optimal weight: 50.0000 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17591 Z= 0.212 Angle : 0.541 9.419 23958 Z= 0.274 Chirality : 0.043 0.200 2644 Planarity : 0.004 0.039 2951 Dihedral : 13.682 178.298 2906 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.53 % Allowed : 14.34 % Favored : 84.13 % 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: -1.79 (0.18), residues: 2071 helix: -0.55 (0.18), residues: 822 sheet: -1.11 (0.28), residues: 279 loop : -1.72 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 152 HIS 0.004 0.001 HIS D 205 PHE 0.014 0.001 PHE A 491 TYR 0.016 0.001 TYR A 265 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 187 average time/residue: 0.3510 time to fit residues: 95.6469 Evaluate side-chains 173 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1563 time to fit residues: 5.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 50.0000 chunk 23 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17591 Z= 0.256 Angle : 0.563 9.511 23958 Z= 0.287 Chirality : 0.044 0.198 2644 Planarity : 0.004 0.039 2951 Dihedral : 13.680 179.464 2906 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.35 % Allowed : 15.20 % Favored : 83.46 % 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: -1.74 (0.18), residues: 2071 helix: -0.47 (0.18), residues: 837 sheet: -0.98 (0.28), residues: 287 loop : -1.78 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 227 HIS 0.004 0.001 HIS D 205 PHE 0.018 0.001 PHE E 159 TYR 0.017 0.001 TYR A 265 ARG 0.005 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.807 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 183 average time/residue: 0.3287 time to fit residues: 89.1465 Evaluate side-chains 172 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1978 time to fit residues: 5.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 18 optimal weight: 0.0670 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 0.0270 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17591 Z= 0.127 Angle : 0.505 8.997 23958 Z= 0.256 Chirality : 0.041 0.219 2644 Planarity : 0.004 0.036 2951 Dihedral : 13.567 178.628 2906 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.86 % Allowed : 15.87 % Favored : 83.27 % 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: -1.37 (0.18), residues: 2071 helix: -0.04 (0.18), residues: 832 sheet: -0.99 (0.29), residues: 280 loop : -1.64 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 596 HIS 0.003 0.001 HIS D 111 PHE 0.009 0.001 PHE A 491 TYR 0.015 0.001 TYR A 684 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.732 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 192 average time/residue: 0.3528 time to fit residues: 99.1186 Evaluate side-chains 178 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2963 time to fit residues: 5.6284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 188 optimal weight: 50.0000 chunk 124 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17591 Z= 0.368 Angle : 0.627 8.544 23958 Z= 0.319 Chirality : 0.046 0.199 2644 Planarity : 0.005 0.038 2951 Dihedral : 13.694 179.311 2906 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.80 % Allowed : 16.48 % Favored : 82.72 % 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: -1.60 (0.18), residues: 2071 helix: -0.28 (0.18), residues: 832 sheet: -0.95 (0.29), residues: 287 loop : -1.76 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 596 HIS 0.005 0.001 HIS A 60 PHE 0.024 0.002 PHE E 159 TYR 0.018 0.002 TYR A 265 ARG 0.007 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.922 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 177 average time/residue: 0.3266 time to fit residues: 86.4871 Evaluate side-chains 171 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1610 time to fit residues: 4.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 210 optimal weight: 30.0000 chunk 193 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17591 Z= 0.163 Angle : 0.538 9.096 23958 Z= 0.271 Chirality : 0.042 0.214 2644 Planarity : 0.004 0.038 2951 Dihedral : 13.620 179.620 2906 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 0.37 % Allowed : 16.79 % Favored : 82.84 % 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: -1.30 (0.18), residues: 2071 helix: 0.07 (0.19), residues: 825 sheet: -0.90 (0.29), residues: 284 loop : -1.65 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 596 HIS 0.003 0.001 HIS C 111 PHE 0.018 0.001 PHE A 59 TYR 0.013 0.001 TYR A 731 ARG 0.004 0.000 ARG A 735 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.827 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 174 average time/residue: 0.3606 time to fit residues: 92.1849 Evaluate side-chains 171 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2872 time to fit residues: 3.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 20.0000 chunk 51 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.194774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144297 restraints weight = 23793.043| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.99 r_work: 0.3232 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17591 Z= 0.190 Angle : 0.544 10.842 23958 Z= 0.272 Chirality : 0.043 0.214 2644 Planarity : 0.004 0.036 2951 Dihedral : 13.566 179.671 2906 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 17.22 % Favored : 82.66 % 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: -1.20 (0.18), residues: 2071 helix: 0.19 (0.19), residues: 825 sheet: -0.86 (0.30), residues: 284 loop : -1.63 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 596 HIS 0.004 0.001 HIS D 205 PHE 0.019 0.001 PHE A 59 TYR 0.017 0.001 TYR A 731 ARG 0.005 0.000 ARG A 735 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.62 seconds wall clock time: 67 minutes 3.92 seconds (4023.92 seconds total)