Starting phenix.real_space_refine on Sun Mar 17 03:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/03_2024/6ww7_21929_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/03_2024/6ww7_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_21929/03_2024/6ww7_21929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/03_2024/6ww7_21929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/03_2024/6ww7_21929_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww7_21929/03_2024/6ww7_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.59, per 1000 atoms: 0.52 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: 6.93 Conformation dependent library (CDL) restraints added in 2.7 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: 2.99 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: 5.69 Time building geometry restraints manager: 7.47 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.500 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 44.960 Find NCS groups from input model: 0.460 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: 58.260 ------------------------------------------------------------------------------- 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 : 1.960 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: A 52 LYS cc_start: 0.8228 (pttt) cc_final: 0.7944 (pttp) REVERT: A 84 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 137 GLN cc_start: 0.8494 (mt0) cc_final: 0.8057 (tm-30) REVERT: A 258 GLN cc_start: 0.7803 (tt0) cc_final: 0.7455 (tt0) REVERT: A 446 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 142 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7065 (tpm170) REVERT: B 254 MET cc_start: 0.5543 (mtp) cc_final: 0.5209 (tmm) REVERT: B 255 LYS cc_start: 0.7368 (ttmt) cc_final: 0.7087 (ttpp) REVERT: C 73 PHE cc_start: 0.8700 (t80) cc_final: 0.8382 (t80) REVERT: E 32 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7726 (ptp90) REVERT: E 70 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: F 81 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8024 (ttp-170) REVERT: F 83 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8481 (Cg_endo) REVERT: H 72 GLU cc_start: 0.7741 (pt0) cc_final: 0.6748 (mm-30) REVERT: H 97 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7149 (mm-30) REVERT: H 114 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.6974 (tpt90) REVERT: H 191 ASP cc_start: 0.6538 (m-30) cc_final: 0.6318 (m-30) REVERT: I 145 GLN cc_start: 0.8597 (tt0) cc_final: 0.8291 (tt0) outliers start: 52 outliers final: 36 residues processed: 360 average time/residue: 0.3737 time to fit residues: 184.3585 Evaluate side-chains 269 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR 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: 7.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 0.0040 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 989 ASN B 194 GLN 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 168 GLN H 199 ASN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN I 171 HIS I 186 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16947 Z= 0.381 Angle : 0.599 13.239 22979 Z= 0.302 Chirality : 0.045 0.203 2598 Planarity : 0.004 0.047 2917 Dihedral : 8.947 69.547 2450 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.10 % Allowed : 17.00 % Favored : 78.90 % 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: -1.61 (0.18), residues: 2030 helix: -0.27 (0.19), residues: 668 sheet: -1.11 (0.22), residues: 506 loop : -1.58 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 171 HIS 0.007 0.001 HIS A 501 PHE 0.018 0.002 PHE A 324 TYR 0.019 0.002 TYR B 44 ARG 0.006 0.001 ARG C 93 *********************** 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 303 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8327 (pttt) cc_final: 0.8034 (ptpp) REVERT: A 84 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7477 (mp0) REVERT: A 137 GLN cc_start: 0.8537 (mt0) cc_final: 0.8106 (tm-30) REVERT: A 258 GLN cc_start: 0.7721 (tt0) cc_final: 0.7423 (tt0) REVERT: A 295 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 446 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 627 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8777 (tt) REVERT: B 142 ARG cc_start: 0.7459 (ttp80) cc_final: 0.6840 (tpm170) REVERT: B 254 MET cc_start: 0.5520 (mtp) cc_final: 0.5299 (tmm) REVERT: E 32 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7593 (ptp90) REVERT: F 20 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7076 (mtm180) REVERT: F 83 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8482 (Cg_endo) REVERT: H 72 GLU cc_start: 0.7762 (pt0) cc_final: 0.6620 (mm-30) REVERT: H 97 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7171 (mm-30) outliers start: 73 outliers final: 50 residues processed: 289 average time/residue: 0.3600 time to fit residues: 145.3457 Evaluate side-chains 266 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 105 ASN I 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16947 Z= 0.177 Angle : 0.510 9.895 22979 Z= 0.257 Chirality : 0.042 0.151 2598 Planarity : 0.003 0.045 2917 Dihedral : 6.850 55.764 2431 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.70 % Allowed : 17.96 % Favored : 78.34 % 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: -1.00 (0.18), residues: 2030 helix: 0.30 (0.20), residues: 670 sheet: -0.78 (0.22), residues: 496 loop : -1.27 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 164 HIS 0.004 0.001 HIS A 501 PHE 0.018 0.001 PHE A 324 TYR 0.026 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 305 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8250 (pttt) cc_final: 0.8035 (ptpp) REVERT: A 84 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7417 (mp0) REVERT: A 137 GLN cc_start: 0.8526 (mt0) cc_final: 0.8095 (tm-30) REVERT: A 258 GLN cc_start: 0.7671 (tt0) cc_final: 0.7393 (tt0) REVERT: A 295 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 446 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 642 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8958 (mp) REVERT: B 142 ARG cc_start: 0.7467 (ttp80) cc_final: 0.6830 (tpm170) REVERT: E 70 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7508 (mtm) REVERT: F 83 PRO cc_start: 0.8709 (Cg_exo) cc_final: 0.8505 (Cg_endo) REVERT: H 72 GLU cc_start: 0.7746 (pt0) cc_final: 0.6543 (mm-30) REVERT: H 77 LEU cc_start: 0.8299 (tt) cc_final: 0.7995 (mp) REVERT: H 97 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7163 (mm-30) REVERT: I 70 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8368 (tmmt) REVERT: I 145 GLN cc_start: 0.8583 (tt0) cc_final: 0.8191 (tt0) outliers start: 66 outliers final: 45 residues processed: 294 average time/residue: 0.3407 time to fit residues: 143.7941 Evaluate side-chains 259 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 262 GLN A 428 HIS A 501 HIS B 194 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16947 Z= 0.264 Angle : 0.532 8.147 22979 Z= 0.270 Chirality : 0.043 0.150 2598 Planarity : 0.004 0.046 2917 Dihedral : 6.064 56.936 2412 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.60 % Allowed : 18.80 % Favored : 76.60 % 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: -0.77 (0.18), residues: 2030 helix: 0.49 (0.21), residues: 670 sheet: -0.68 (0.22), residues: 509 loop : -1.11 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 164 HIS 0.005 0.001 HIS A 501 PHE 0.014 0.001 PHE A 202 TYR 0.032 0.001 TYR G 148 ARG 0.008 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 300 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 218 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8372 (pttt) cc_final: 0.8067 (ptpp) REVERT: A 84 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 137 GLN cc_start: 0.8538 (mt0) cc_final: 0.8108 (tm-30) REVERT: A 446 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 642 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8967 (mp) REVERT: B 142 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6812 (tpm170) REVERT: C 9 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7893 (p0) REVERT: F 83 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8481 (Cg_endo) REVERT: H 16 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8545 (mp) REVERT: H 97 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7176 (mm-30) REVERT: H 145 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6007 (mm-30) REVERT: H 147 HIS cc_start: 0.4133 (OUTLIER) cc_final: 0.2682 (p90) REVERT: I 105 ASN cc_start: 0.8343 (t0) cc_final: 0.7962 (t0) REVERT: I 169 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.7403 (mtm-85) outliers start: 82 outliers final: 55 residues processed: 285 average time/residue: 0.3489 time to fit residues: 143.0617 Evaluate side-chains 264 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 205 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 927 SER Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS A 501 HIS B 269 GLN C 46 GLN ** 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 I 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1840 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= 0.242 Angle : 0.527 7.665 22979 Z= 0.268 Chirality : 0.043 0.151 2598 Planarity : 0.004 0.045 2917 Dihedral : 5.969 57.119 2411 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.94 % Allowed : 19.36 % 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: -0.59 (0.19), residues: 2030 helix: 0.62 (0.21), residues: 667 sheet: -0.55 (0.23), residues: 508 loop : -1.00 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 580 PHE 0.019 0.001 PHE A 324 TYR 0.023 0.001 TYR G 148 ARG 0.006 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 312 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 224 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8380 (pttt) cc_final: 0.8076 (ptpp) REVERT: A 84 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7437 (mp0) REVERT: A 137 GLN cc_start: 0.8547 (mt0) cc_final: 0.8117 (tm-30) REVERT: A 295 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7783 (mt) REVERT: A 446 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 488 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7367 (mt) REVERT: A 627 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 642 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8978 (mp) REVERT: B 142 ARG cc_start: 0.7490 (ttp80) cc_final: 0.6813 (tpm170) REVERT: B 224 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7891 (mtt-85) REVERT: C 9 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7878 (p0) REVERT: C 157 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: C 219 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7565 (mmtt) REVERT: E 70 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7534 (mtm) REVERT: F 20 ARG cc_start: 0.7506 (mtm110) cc_final: 0.7303 (mtm180) REVERT: F 81 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7998 (ttp-170) REVERT: H 16 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8572 (mp) REVERT: H 97 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7532 (tm-30) REVERT: H 145 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6139 (mm-30) REVERT: H 147 HIS cc_start: 0.4147 (OUTLIER) cc_final: 0.2690 (p90) REVERT: I 105 ASN cc_start: 0.8317 (t0) cc_final: 0.7968 (t0) REVERT: I 180 LEU cc_start: 0.8428 (tp) cc_final: 0.7784 (pp) outliers start: 88 outliers final: 60 residues processed: 294 average time/residue: 0.3367 time to fit residues: 139.9153 Evaluate side-chains 282 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 212 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS C 46 GLN ** 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 I 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16947 Z= 0.203 Angle : 0.512 7.236 22979 Z= 0.261 Chirality : 0.042 0.249 2598 Planarity : 0.004 0.050 2917 Dihedral : 5.814 58.226 2410 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.38 % Allowed : 20.37 % Favored : 75.25 % 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: -0.44 (0.19), residues: 2030 helix: 0.73 (0.21), residues: 667 sheet: -0.44 (0.23), residues: 502 loop : -0.92 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 PHE 0.016 0.001 PHE I 201 TYR 0.019 0.001 TYR G 148 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 301 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8385 (pttt) cc_final: 0.8050 (ptpp) REVERT: A 84 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7440 (mp0) REVERT: A 137 GLN cc_start: 0.8550 (mt0) cc_final: 0.8128 (tm-30) REVERT: A 446 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 488 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7328 (mt) REVERT: A 627 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 642 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 660 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6597 (ttm110) REVERT: A 881 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7631 (mtp85) REVERT: B 142 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6818 (tpm170) REVERT: B 224 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7865 (mtt-85) REVERT: C 9 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7773 (p0) REVERT: C 157 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.5996 (pm20) REVERT: C 219 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7544 (mmtt) REVERT: E 70 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7500 (mtm) REVERT: F 20 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7331 (mtm180) REVERT: F 81 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8020 (ttp-170) REVERT: H 16 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8562 (mp) REVERT: H 72 GLU cc_start: 0.7755 (pt0) cc_final: 0.6596 (mm-30) REVERT: H 97 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7162 (mm-30) REVERT: H 145 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6011 (mm-30) REVERT: H 147 HIS cc_start: 0.4195 (OUTLIER) cc_final: 0.2723 (p90) REVERT: H 197 TRP cc_start: 0.7459 (p90) cc_final: 0.6744 (p90) REVERT: I 105 ASN cc_start: 0.8336 (t0) cc_final: 0.8028 (t0) REVERT: I 180 LEU cc_start: 0.8438 (tp) cc_final: 0.7812 (pp) outliers start: 78 outliers final: 55 residues processed: 285 average time/residue: 0.3379 time to fit residues: 137.4735 Evaluate side-chains 276 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 191 THR 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: 8.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 0.0670 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 371 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16947 Z= 0.162 Angle : 0.508 9.502 22979 Z= 0.255 Chirality : 0.042 0.216 2598 Planarity : 0.003 0.053 2917 Dihedral : 5.619 55.409 2410 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.76 % Allowed : 21.49 % Favored : 74.75 % 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: -0.25 (0.19), residues: 2030 helix: 0.90 (0.21), residues: 666 sheet: -0.33 (0.23), residues: 501 loop : -0.81 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 187 HIS 0.003 0.001 HIS A 580 PHE 0.015 0.001 PHE I 201 TYR 0.020 0.001 TYR A 179 ARG 0.007 0.000 ARG G 50 *********************** 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 286 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 219 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7428 (mp0) REVERT: A 137 GLN cc_start: 0.8547 (mt0) cc_final: 0.8122 (tm-30) REVERT: A 446 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 627 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (tt) REVERT: A 642 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8955 (mp) REVERT: A 660 ARG cc_start: 0.7169 (mmm-85) cc_final: 0.6610 (ttm110) REVERT: B 142 ARG cc_start: 0.7435 (ttp80) cc_final: 0.6798 (tpm170) REVERT: B 224 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7881 (mtt-85) REVERT: C 9 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7737 (p0) REVERT: C 157 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.5905 (pm20) REVERT: C 219 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7521 (mmtt) REVERT: E 70 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: F 81 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7991 (ttp-170) REVERT: H 16 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8571 (mp) REVERT: H 72 GLU cc_start: 0.7697 (pt0) cc_final: 0.6564 (mm-30) REVERT: H 77 LEU cc_start: 0.8374 (tt) cc_final: 0.7998 (mt) REVERT: H 97 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7152 (mm-30) REVERT: H 145 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6080 (mm-30) REVERT: H 147 HIS cc_start: 0.4150 (OUTLIER) cc_final: 0.2631 (p90) REVERT: H 197 TRP cc_start: 0.7392 (p90) cc_final: 0.6652 (p90) REVERT: I 105 ASN cc_start: 0.8315 (t0) cc_final: 0.8057 (t0) REVERT: I 180 LEU cc_start: 0.8503 (tp) cc_final: 0.7824 (pp) outliers start: 67 outliers final: 51 residues processed: 272 average time/residue: 0.3443 time to fit residues: 133.5605 Evaluate side-chains 272 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.0570 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 435 GLN ** 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 I 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16947 Z= 0.164 Angle : 0.514 8.208 22979 Z= 0.260 Chirality : 0.042 0.216 2598 Planarity : 0.004 0.056 2917 Dihedral : 5.473 55.329 2407 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.70 % Allowed : 21.77 % Favored : 74.52 % 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: -0.10 (0.19), residues: 2030 helix: 0.99 (0.21), residues: 666 sheet: -0.22 (0.23), residues: 501 loop : -0.72 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 187 HIS 0.003 0.000 HIS A 580 PHE 0.017 0.001 PHE A 324 TYR 0.023 0.001 TYR A 179 ARG 0.008 0.000 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 296 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7183 (ptm-80) REVERT: A 84 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7427 (mp0) REVERT: A 137 GLN cc_start: 0.8546 (mt0) cc_final: 0.8126 (tm-30) REVERT: A 446 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 488 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7350 (mt) REVERT: A 627 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 642 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8951 (mp) REVERT: A 660 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6601 (ttm110) REVERT: B 60 MET cc_start: 0.8142 (ttt) cc_final: 0.7927 (ttt) REVERT: B 142 ARG cc_start: 0.7413 (ttp80) cc_final: 0.6788 (tpm170) REVERT: B 224 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7942 (mtt-85) REVERT: C 9 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7729 (p0) REVERT: C 157 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.5823 (pm20) REVERT: C 219 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7510 (mmtt) REVERT: E 70 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7475 (mtm) REVERT: F 20 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7188 (mtm110) REVERT: F 81 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7999 (ttp-170) REVERT: G 117 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8636 (mtpt) REVERT: H 16 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8562 (mp) REVERT: H 65 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4110 (mm) REVERT: H 72 GLU cc_start: 0.7694 (pt0) cc_final: 0.6630 (mm-30) REVERT: H 97 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7183 (mm-30) REVERT: H 145 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6052 (mm-30) REVERT: H 147 HIS cc_start: 0.4142 (OUTLIER) cc_final: 0.2589 (p90) REVERT: I 105 ASN cc_start: 0.8311 (t0) cc_final: 0.8077 (t0) REVERT: I 180 LEU cc_start: 0.8536 (tp) cc_final: 0.7844 (pp) outliers start: 66 outliers final: 53 residues processed: 282 average time/residue: 0.3407 time to fit residues: 135.9779 Evaluate side-chains 281 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 218 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 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** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 HIS I 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16947 Z= 0.258 Angle : 0.556 8.829 22979 Z= 0.279 Chirality : 0.044 0.216 2598 Planarity : 0.004 0.044 2917 Dihedral : 5.575 56.061 2407 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.15 % Allowed : 21.55 % Favored : 74.30 % 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: -0.20 (0.19), residues: 2030 helix: 0.85 (0.21), residues: 674 sheet: -0.26 (0.23), residues: 511 loop : -0.76 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 164 HIS 0.003 0.001 HIS A 580 PHE 0.017 0.001 PHE A 324 TYR 0.023 0.001 TYR A 179 ARG 0.008 0.000 ARG A 275 *********************** 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 293 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 219 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7422 (ptm-80) REVERT: A 137 GLN cc_start: 0.8553 (mt0) cc_final: 0.8156 (tm-30) REVERT: A 446 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 488 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7372 (mt) REVERT: A 627 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 642 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 660 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6675 (ttm110) REVERT: B 142 ARG cc_start: 0.7453 (ttp80) cc_final: 0.6793 (tpm170) REVERT: B 224 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7962 (mtt-85) REVERT: C 9 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7728 (p0) REVERT: C 157 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.5746 (pm20) REVERT: C 219 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7510 (mmtt) REVERT: E 70 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: F 81 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7973 (ttp-170) REVERT: H 16 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8578 (mp) REVERT: H 65 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.4106 (mm) REVERT: H 72 GLU cc_start: 0.7548 (pt0) cc_final: 0.6487 (mm-30) REVERT: H 77 LEU cc_start: 0.8393 (tt) cc_final: 0.7945 (mt) REVERT: H 97 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7211 (mm-30) REVERT: H 145 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6046 (mm-30) REVERT: H 147 HIS cc_start: 0.4123 (OUTLIER) cc_final: 0.2601 (p90) REVERT: I 105 ASN cc_start: 0.8373 (t0) cc_final: 0.8100 (t0) REVERT: I 180 LEU cc_start: 0.8534 (tp) cc_final: 0.7846 (pp) outliers start: 74 outliers final: 60 residues processed: 280 average time/residue: 0.3427 time to fit residues: 136.9964 Evaluate side-chains 285 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 948 TYR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 147 HIS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 208 HIS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.091 > 50: distance: 12 - 15: 13.625 distance: 15 - 16: 15.287 distance: 16 - 17: 10.562 distance: 16 - 19: 9.520 distance: 17 - 18: 8.920 distance: 17 - 22: 3.923 distance: 19 - 20: 27.254 distance: 19 - 21: 4.347 distance: 22 - 23: 12.107 distance: 23 - 24: 9.669 distance: 23 - 26: 15.477 distance: 24 - 25: 7.840 distance: 24 - 29: 8.105 distance: 26 - 27: 21.489 distance: 26 - 28: 33.963 distance: 29 - 30: 23.882 distance: 29 - 35: 25.469 distance: 30 - 31: 3.995 distance: 30 - 33: 23.390 distance: 31 - 32: 9.359 distance: 31 - 36: 13.456 distance: 33 - 34: 11.373 distance: 34 - 35: 38.010 distance: 36 - 37: 12.518 distance: 37 - 38: 12.605 distance: 38 - 39: 13.026 distance: 38 - 40: 7.333 distance: 40 - 41: 8.376 distance: 41 - 42: 19.712 distance: 41 - 44: 19.309 distance: 42 - 43: 7.473 distance: 42 - 47: 39.157 distance: 44 - 45: 19.532 distance: 44 - 46: 8.395 distance: 47 - 48: 19.984 distance: 48 - 49: 12.884 distance: 48 - 51: 22.048 distance: 49 - 56: 17.229 distance: 51 - 52: 15.253 distance: 52 - 53: 8.247 distance: 53 - 54: 31.703 distance: 54 - 55: 7.672 distance: 56 - 57: 21.995 distance: 56 - 62: 27.863 distance: 57 - 58: 25.272 distance: 57 - 60: 39.507 distance: 58 - 59: 11.722 distance: 58 - 63: 19.474 distance: 61 - 62: 18.406 distance: 63 - 64: 24.180 distance: 64 - 65: 18.185 distance: 64 - 67: 11.195 distance: 65 - 66: 7.827 distance: 65 - 72: 15.996 distance: 67 - 68: 9.266 distance: 68 - 69: 21.200 distance: 69 - 70: 5.935 distance: 69 - 71: 31.981 distance: 72 - 73: 14.428 distance: 73 - 74: 9.568 distance: 73 - 76: 7.097 distance: 74 - 75: 17.962 distance: 74 - 80: 4.928 distance: 76 - 77: 9.827 distance: 77 - 78: 25.531 distance: 77 - 79: 14.253 distance: 80 - 81: 6.967 distance: 81 - 82: 4.844 distance: 81 - 84: 7.675 distance: 82 - 94: 8.998 distance: 84 - 85: 6.614 distance: 85 - 86: 4.597 distance: 85 - 87: 11.891 distance: 86 - 88: 6.498 distance: 87 - 89: 7.734 distance: 87 - 90: 8.081 distance: 88 - 89: 14.130 distance: 89 - 91: 3.184 distance: 91 - 93: 11.434 distance: 92 - 93: 7.809