Starting phenix.real_space_refine on Mon Dec 11 03:43:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/12_2023/6ww7_21929_updated.pdb" } resolution = 3.4 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= 0.001 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 10610 2.51 5 N 2853 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 593": "OD1" <-> "OD2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 884": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A GLU 930": "OE1" <-> "OE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ASP 159": "OD1" <-> "OD2" Residue "H TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H ASP 163": "OD1" <-> "OD2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "I PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I ASP 100": "OD1" <-> "OD2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 175": "OD1" <-> "OD2" Residue "I GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16576 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7347 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 883} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2306 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 276} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1707 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 67 Classifications: {'peptide': 14} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 11} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 97} 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: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 774 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 884 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "H" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1462 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 2 Chain: "I" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1150 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.92, per 1000 atoms: 0.54 Number of scatterers: 16576 At special positions: 0 Unit cell: (94.468, 124.564, 213.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 3051 8.00 N 2853 7.00 C 10610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.04 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG I 301 " - " ASN I 182 " " NAG J 1 " - " ASN A 818 " " NAG K 1 " - " ASN A 913 " Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 3.1 seconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 22 sheets defined 31.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.711A pdb=" N GLU A 451 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 480 through 501 Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 906 through 908 No H-bonds generated for 'chain 'A' and resid 906 through 908' Processing helix chain 'A' and resid 962 through 991 removed outlier: 4.079A pdb=" N PHE A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.789A pdb=" N ASP B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.590A pdb=" N VAL B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 69 through 82 removed outlier: 4.557A pdb=" N PHE B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 79 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.150A pdb=" N ILE B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.781A pdb=" N ILE B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.749A pdb=" N ARG B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 167 removed outlier: 3.583A pdb=" N ALA B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.538A pdb=" N ALA B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 205 through 221 removed outlier: 4.826A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 247 through 274 removed outlier: 3.701A pdb=" N GLN B 263 " --> pdb=" O TRP B 259 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 288 removed outlier: 4.605A pdb=" N GLU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.757A pdb=" N GLY C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 64 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 87 through 90 No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 115 through 131 Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 146 through 152 Proline residue: C 150 - end of helix Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 183 through 186 No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 214 through 225 removed outlier: 4.281A pdb=" N LYS C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'E' and resid 4 through 34 removed outlier: 4.151A pdb=" N LYS E 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 34 " --> pdb=" O MET E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 63 removed outlier: 3.551A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 97 through 100 No H-bonds generated for 'chain 'E' and resid 97 through 100' Processing helix chain 'F' and resid 16 through 44 removed outlier: 3.836A pdb=" N GLY F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 70 removed outlier: 3.553A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 56 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 86 No H-bonds generated for 'chain 'F' and resid 83 through 86' Processing helix chain 'F' and resid 89 through 107 removed outlier: 3.777A pdb=" N THR F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 8 through 20 Processing helix chain 'H' and resid 68 through 82 removed outlier: 3.546A pdb=" N LEU H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR H 76 " --> pdb=" O GLU H 72 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.724A pdb=" N ARG H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 175 Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 200 through 208 removed outlier: 3.839A pdb=" N ALA H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS H 208 " --> pdb=" O LYS H 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 103 Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 199 through 205 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.948A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A 75 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 87 through 93 removed outlier: 6.541A pdb=" N VAL A 100 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET A 90 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 98 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 92 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU A 111 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 117 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 134 removed outlier: 6.732A pdb=" N LEU A 146 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 131 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA A 144 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 133 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 142 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 174 through 180 removed outlier: 6.800A pdb=" N LEU A 189 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 178 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER A 180 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 185 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.515A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.704A pdb=" N LEU A 295 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS A 306 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 390 through 394 removed outlier: 3.772A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N CYS A 338 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR A 319 " --> pdb=" O CYS A 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 402 through 411 removed outlier: 6.465A pdb=" N GLN A 424 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 405 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 422 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 407 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 420 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 409 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 418 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 452 through 459 removed outlier: 6.892A pdb=" N VAL A 539 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 455 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 537 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A 457 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A 535 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.546A pdb=" N THR A 588 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL A 574 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 572 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 592 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE A 570 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 625 through 628 removed outlier: 3.690A pdb=" N GLN A 625 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 670 through 675 removed outlier: 6.001A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 723 through 725 Processing sheet with id= O, first strand: chain 'A' and resid 705 through 712 removed outlier: 6.756A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLY A 712 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU A 740 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 756 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 783 through 786 removed outlier: 3.636A pdb=" N HIS A 783 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 846 through 849 Processing sheet with id= R, first strand: chain 'G' and resid 47 through 50 Processing sheet with id= S, first strand: chain 'G' and resid 74 through 77 Processing sheet with id= T, first strand: chain 'H' and resid 151 through 153 removed outlier: 4.006A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU H 30 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR H 92 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY H 28 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN H 94 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL H 26 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN H 27 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE H 61 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU H 29 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 31 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N CYS H 57 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 127 through 133 removed outlier: 6.214A pdb=" N LEU I 55 " --> pdb=" O PRO I 113 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS I 58 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS I 70 " --> pdb=" O HIS I 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR I 82 " --> pdb=" O ASN I 77 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 182 through 188 642 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2692 1.31 - 1.44: 4603 1.44 - 1.57: 9549 1.57 - 1.70: 0 1.70 - 1.83: 103 Bond restraints: 16947 Sorted by residual: bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.456 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C7 NAG A1001 " pdb=" N2 NAG A1001 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C7 NAG I 301 " pdb=" N2 NAG I 301 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 16942 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.39: 464 106.39 - 113.30: 9285 113.30 - 120.21: 6114 120.21 - 127.12: 6905 127.12 - 134.03: 211 Bond angle restraints: 22979 Sorted by residual: angle pdb=" N ILE B 128 " pdb=" CA ILE B 128 " pdb=" C ILE B 128 " ideal model delta sigma weight residual 113.42 108.76 4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" C VAL A 230 " pdb=" N ASP A 231 " pdb=" CA ASP A 231 " ideal model delta sigma weight residual 120.82 125.61 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" N SER C 40 " pdb=" CA SER C 40 " pdb=" C SER C 40 " ideal model delta sigma weight residual 108.07 112.51 -4.44 1.59e+00 3.96e-01 7.80e+00 angle pdb=" N VAL A 453 " pdb=" CA VAL A 453 " pdb=" C VAL A 453 " ideal model delta sigma weight residual 112.96 110.28 2.68 1.00e+00 1.00e+00 7.19e+00 angle pdb=" N ASP A 231 " pdb=" CA ASP A 231 " pdb=" C ASP A 231 " ideal model delta sigma weight residual 111.37 115.77 -4.40 1.65e+00 3.67e-01 7.12e+00 ... (remaining 22974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 9328 21.55 - 43.11: 714 43.11 - 64.66: 97 64.66 - 86.22: 34 86.22 - 107.77: 15 Dihedral angle restraints: 10188 sinusoidal: 4152 harmonic: 6036 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 368 " pdb=" CB CYS A 368 " ideal model delta sinusoidal sigma weight residual -86.00 -134.12 48.12 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA VAL A 230 " pdb=" C VAL A 230 " pdb=" N ASP A 231 " pdb=" CA ASP A 231 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS A 227 " pdb=" SG CYS A 227 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual 93.00 59.72 33.28 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 10185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1647 0.032 - 0.065: 659 0.065 - 0.097: 175 0.097 - 0.130: 108 0.130 - 0.162: 9 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C5 NAG A1001 " pdb=" C4 NAG A1001 " pdb=" C6 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.41 -2.57 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C5 NAG K 1 " pdb=" C4 NAG K 1 " pdb=" C6 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.56 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" C5 NAG I 301 " pdb=" C4 NAG I 301 " pdb=" C6 NAG I 301 " pdb=" O5 NAG I 301 " both_signs ideal model delta sigma weight residual False -2.41 -2.55 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2595 not shown) Planarity restraints: 2921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 18 " -0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 19 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 19 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 19 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 565 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.42e+00 pdb=" N PRO A 566 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 132 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO I 133 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " -0.016 5.00e-02 4.00e+02 ... (remaining 2918 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 401 2.70 - 3.25: 15863 3.25 - 3.80: 25449 3.80 - 4.35: 34293 4.35 - 4.90: 57969 Nonbonded interactions: 133975 Sorted by model distance: nonbonded pdb=" O SER A 927 " pdb=" OG SER A 927 " model vdw 2.145 2.440 nonbonded pdb=" O THR C 137 " pdb=" OH TYR F 110 " model vdw 2.145 2.440 nonbonded pdb=" O TRP A 992 " pdb=" OG SER B 86 " model vdw 2.175 2.440 nonbonded pdb=" O PRO C 141 " pdb=" OG1 THR F 47 " model vdw 2.192 2.440 nonbonded pdb=" O ALA A 975 " pdb=" OG1 THR A 979 " model vdw 2.221 2.440 ... (remaining 133970 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 'J' selection = chain 'K' } 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: 1.600 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: 7.420 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 45.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 0.112 16947 Z= 0.303 Angle : 0.580 6.032 22979 Z= 0.335 Chirality : 0.042 0.162 2598 Planarity : 0.003 0.041 2917 Dihedral : 15.894 107.771 6284 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 12.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -2.34 (0.17), residues: 2030 helix: -1.13 (0.18), residues: 663 sheet: -1.42 (0.21), residues: 506 loop : -1.83 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.005 0.001 HIS I 58 PHE 0.013 0.001 PHE A 202 TYR 0.010 0.001 TYR A 938 ARG 0.002 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 1.859 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: 52 outliers final: 36 residues processed: 360 average time/residue: 0.3876 time to fit residues: 191.5137 Evaluate side-chains 264 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1509 time to fit residues: 12.4872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 304 GLN A 408 GLN A 424 GLN A 466 GLN A 501 HIS A 794 GLN A 989 ASN C 39 GLN C 46 GLN E 27 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN H 208 HIS I 87 GLN I 105 ASN I 171 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16947 Z= 0.299 Angle : 0.571 13.752 22979 Z= 0.287 Chirality : 0.044 0.223 2598 Planarity : 0.004 0.042 2917 Dihedral : 7.755 73.191 2383 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.13 % Allowed : 17.96 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -1.46 (0.18), residues: 2030 helix: -0.14 (0.20), residues: 666 sheet: -1.06 (0.22), residues: 508 loop : -1.46 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 171 HIS 0.010 0.001 HIS I 58 PHE 0.017 0.001 PHE A 324 TYR 0.022 0.001 TYR B 44 ARG 0.006 0.001 ARG H 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 1.928 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: 38 outliers final: 20 residues processed: 262 average time/residue: 0.3778 time to fit residues: 138.2224 Evaluate side-chains 242 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 2.084 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1545 time to fit residues: 8.4247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS C 46 GLN C 230 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16947 Z= 0.216 Angle : 0.517 9.654 22979 Z= 0.262 Chirality : 0.042 0.151 2598 Planarity : 0.004 0.048 2917 Dihedral : 5.661 56.079 2383 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.36 % Allowed : 18.86 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2030 helix: 0.33 (0.20), residues: 669 sheet: -0.82 (0.22), residues: 502 loop : -1.19 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 443 HIS 0.008 0.001 HIS I 58 PHE 0.019 0.001 PHE A 324 TYR 0.023 0.001 TYR G 148 ARG 0.007 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 266 average time/residue: 0.3655 time to fit residues: 136.9043 Evaluate side-chains 228 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1718 time to fit residues: 9.2955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 0.0980 chunk 96 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 HIS A 501 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16947 Z= 0.247 Angle : 0.525 8.178 22979 Z= 0.268 Chirality : 0.043 0.150 2598 Planarity : 0.004 0.045 2917 Dihedral : 5.244 56.748 2383 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.53 % Allowed : 20.03 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2030 helix: 0.51 (0.21), residues: 669 sheet: -0.73 (0.22), residues: 503 loop : -1.07 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 164 HIS 0.007 0.001 HIS I 58 PHE 0.014 0.001 PHE A 202 TYR 0.030 0.001 TYR G 148 ARG 0.007 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.827 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: 45 outliers final: 20 residues processed: 250 average time/residue: 0.3688 time to fit residues: 129.7949 Evaluate side-chains 226 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1538 time to fit residues: 8.2574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS A 428 HIS A 501 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN I 87 GLN I 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16947 Z= 0.147 Angle : 0.497 7.160 22979 Z= 0.255 Chirality : 0.041 0.166 2598 Planarity : 0.003 0.041 2917 Dihedral : 4.969 55.570 2383 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.29 % Allowed : 21.32 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 2030 helix: 0.76 (0.21), residues: 668 sheet: -0.43 (0.23), residues: 508 loop : -0.87 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 164 HIS 0.006 0.001 HIS I 58 PHE 0.017 0.001 PHE A 324 TYR 0.021 0.001 TYR G 148 ARG 0.007 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 233 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 251 average time/residue: 0.3788 time to fit residues: 132.3746 Evaluate side-chains 222 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1750 time to fit residues: 5.3578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.3980 chunk 177 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16947 Z= 0.177 Angle : 0.517 11.053 22979 Z= 0.263 Chirality : 0.042 0.152 2598 Planarity : 0.003 0.042 2917 Dihedral : 4.897 55.725 2383 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.12 % Allowed : 22.67 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2030 helix: 0.88 (0.21), residues: 666 sheet: -0.33 (0.23), residues: 514 loop : -0.83 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 187 HIS 0.008 0.001 HIS H 189 PHE 0.019 0.001 PHE C 73 TYR 0.021 0.001 TYR A 179 ARG 0.009 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 239 average time/residue: 0.3790 time to fit residues: 126.8744 Evaluate side-chains 215 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1612 time to fit residues: 4.5743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN A 501 HIS ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16947 Z= 0.182 Angle : 0.515 8.989 22979 Z= 0.262 Chirality : 0.042 0.158 2598 Planarity : 0.003 0.041 2917 Dihedral : 4.835 55.603 2383 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.23 % Allowed : 22.67 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2030 helix: 0.93 (0.21), residues: 666 sheet: -0.26 (0.23), residues: 510 loop : -0.74 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 187 HIS 0.006 0.001 HIS I 58 PHE 0.017 0.001 PHE A 324 TYR 0.022 0.001 TYR A 179 ARG 0.008 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 227 average time/residue: 0.3771 time to fit residues: 120.4139 Evaluate side-chains 218 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1681 time to fit residues: 6.8954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN B 42 ASN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16947 Z= 0.315 Angle : 0.582 11.616 22979 Z= 0.296 Chirality : 0.044 0.162 2598 Planarity : 0.004 0.045 2917 Dihedral : 5.116 56.759 2383 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.95 % Allowed : 22.62 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2030 helix: 0.71 (0.21), residues: 674 sheet: -0.37 (0.23), residues: 508 loop : -0.80 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 164 HIS 0.007 0.001 HIS I 58 PHE 0.019 0.001 PHE I 201 TYR 0.023 0.002 TYR G 148 ARG 0.007 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 235 average time/residue: 0.3818 time to fit residues: 125.8282 Evaluate side-chains 226 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1671 time to fit residues: 5.9625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 435 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16947 Z= 0.178 Angle : 0.532 8.034 22979 Z= 0.271 Chirality : 0.042 0.156 2598 Planarity : 0.004 0.042 2917 Dihedral : 4.932 55.118 2383 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.22 % Allowed : 23.68 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2030 helix: 0.86 (0.21), residues: 670 sheet: -0.27 (0.23), residues: 512 loop : -0.71 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 164 HIS 0.006 0.001 HIS I 58 PHE 0.017 0.001 PHE I 201 TYR 0.024 0.001 TYR A 179 ARG 0.009 0.000 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 224 average time/residue: 0.3781 time to fit residues: 119.1777 Evaluate side-chains 212 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1637 time to fit residues: 2.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 0.0770 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16947 Z= 0.244 Angle : 0.570 10.723 22979 Z= 0.286 Chirality : 0.043 0.168 2598 Planarity : 0.004 0.045 2917 Dihedral : 4.978 55.784 2383 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.45 % Allowed : 24.13 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2030 helix: 0.78 (0.21), residues: 676 sheet: -0.30 (0.23), residues: 512 loop : -0.68 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 164 HIS 0.006 0.001 HIS I 58 PHE 0.018 0.001 PHE I 201 TYR 0.025 0.001 TYR A 179 ARG 0.009 0.001 ARG A 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 221 average time/residue: 0.3811 time to fit residues: 118.2886 Evaluate side-chains 216 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1721 time to fit residues: 3.9990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122187 restraints weight = 22164.814| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.20 r_work: 0.3193 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16947 Z= 0.201 Angle : 0.558 12.206 22979 Z= 0.279 Chirality : 0.043 0.161 2598 Planarity : 0.004 0.048 2917 Dihedral : 4.925 55.309 2383 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.22 % Allowed : 24.07 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2030 helix: 0.83 (0.21), residues: 676 sheet: -0.28 (0.23), residues: 514 loop : -0.65 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 164 HIS 0.006 0.001 HIS I 58 PHE 0.015 0.001 PHE H 61 TYR 0.025 0.001 TYR A 179 ARG 0.010 0.001 ARG A 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3952.50 seconds wall clock time: 72 minutes 9.78 seconds (4329.78 seconds total)