Starting phenix.real_space_refine on Sat Mar 16 06:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwl_12634/03_2024/7nwl_12634.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Mn 7 7.51 5 S 59 5.16 5 C 8715 2.51 5 N 2291 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1156": "OD1" <-> "OD2" Residue "C GLU 1191": "OE1" <-> "OE2" Residue "C PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1358": "NH1" <-> "NH2" Residue "C ARG 1371": "NH1" <-> "NH2" Residue "C GLU 1372": "OE1" <-> "OE2" Residue "C ARG 1379": "NH1" <-> "NH2" Residue "C ARG 1403": "NH1" <-> "NH2" Residue "C ARG 1421": "NH1" <-> "NH2" Residue "C GLU 1424": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E GLU 157": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4583 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 39, 'TRANS': 563} Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3430 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "C" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2820 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 333} Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "E" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1276 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 153} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.77, per 1000 atoms: 0.56 Number of scatterers: 13904 At special positions: 0 Unit cell: (173, 186.84, 168.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 7 24.99 S 59 16.00 O 2832 8.00 N 2291 7.00 C 8715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.83 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.04 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 55 " distance=2.25 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 6 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " BETA1-2 " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG F 1 " - " ASN A 43 " " NAG G 1 " - " ASN A 141 " " NAG H 1 " - " ASN A 256 " " NAG I 1 " - " ASN A 266 " " NAG J 1 " - " ASN A 275 " " NAG K 1 " - " ASN A 568 " " NAG L 1 " - " ASN B 249 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 397 " Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 2.5 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 33 sheets defined 15.5% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.598A pdb=" N SER A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.696A pdb=" N ASN B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.911A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 19 " --> pdb=" O CYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.745A pdb=" N LYS B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.501A pdb=" N LYS B 136 " --> pdb=" O TYR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 157 removed outlier: 3.845A pdb=" N THR B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.845A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.724A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.819A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 4.152A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.782A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.578A pdb=" N GLY B 384 " --> pdb=" O CYS B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1185 No H-bonds generated for 'chain 'C' and resid 1183 through 1185' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 114 through 123 removed outlier: 3.514A pdb=" N GLU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 164 removed outlier: 3.592A pdb=" N LYS D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix removed outlier: 3.511A pdb=" N LYS D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Proline residue: D 156 - end of helix Processing helix chain 'E' and resid 111 through 116 removed outlier: 3.837A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 116 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 116' Processing helix chain 'E' and resid 119 through 159 removed outlier: 3.916A pdb=" N ASP E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Proline residue: E 132 - end of helix Proline residue: E 151 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.704A pdb=" N ASP A 432 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 422 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.892A pdb=" N SER A 22 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.571A pdb=" N THR A 104 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.855A pdb=" N ASP A 130 " --> pdb=" O TRP A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.995A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.053A pdb=" N SER A 234 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 removed outlier: 3.611A pdb=" N GLN A 319 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.907A pdb=" N SER A 354 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.675A pdb=" N ARG A 544 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 486 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 464 through 465 removed outlier: 3.600A pdb=" N PHE A 465 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.700A pdb=" N TRP B 27 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.555A pdb=" N ILE B 437 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 109 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 3.709A pdb=" N VAL B 202 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 164 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER B 204 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 162 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 206 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE B 160 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 167 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ALA B 336 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 313 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY B 338 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE B 315 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.899A pdb=" N SER B 360 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1150 through 1152 removed outlier: 3.813A pdb=" N GLU C1152 " --> pdb=" O THR C1161 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR C1161 " --> pdb=" O GLU C1152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C1160 " --> pdb=" O PHE C1203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1190 through 1195 Processing sheet with id=AC1, first strand: chain 'C' and resid 1190 through 1195 Processing sheet with id=AC2, first strand: chain 'C' and resid 1240 through 1245 removed outlier: 4.990A pdb=" N ASP C1241 " --> pdb=" O ALA C1257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C1257 " --> pdb=" O ASP C1241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C1253 " --> pdb=" O THR C1245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1281 through 1285 removed outlier: 3.520A pdb=" N LEU C1268 " --> pdb=" O SER C1308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1281 through 1285 removed outlier: 3.520A pdb=" N LEU C1268 " --> pdb=" O SER C1308 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1331 through 1336 removed outlier: 5.536A pdb=" N GLY C1332 " --> pdb=" O ILE C1348 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C1348 " --> pdb=" O GLY C1332 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C1382 " --> pdb=" O VAL C1345 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1372 through 1376 Processing sheet with id=AC7, first strand: chain 'C' and resid 1372 through 1376 Processing sheet with id=AC8, first strand: chain 'C' and resid 1421 through 1428 removed outlier: 3.763A pdb=" N ARG C1421 " --> pdb=" O ASP C1438 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU C1423 " --> pdb=" O SER C1436 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER C1436 " --> pdb=" O LEU C1423 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C1425 " --> pdb=" O LEU C1434 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C1434 " --> pdb=" O VAL C1425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1461 through 1466 removed outlier: 3.638A pdb=" N ILE C1449 " --> pdb=" O PHE C1463 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR C1446 " --> pdb=" O VAL C1490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 58 removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 35 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 96 " --> pdb=" O ALA D 100B" (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA D 100B" --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 58 removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 35 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.519A pdb=" N SER E 65 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 104 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 104 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1344 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: 5.62 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2473 1.32 - 1.45: 3663 1.45 - 1.57: 7978 1.57 - 1.69: 0 1.69 - 1.82: 85 Bond restraints: 14199 Sorted by residual: bond pdb=" CA PRO E 59 " pdb=" C PRO E 59 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" N VAL E 83 " pdb=" CA VAL E 83 " ideal model delta sigma weight residual 1.461 1.502 -0.042 1.08e-02 8.57e+03 1.50e+01 bond pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.49e+01 bond pdb=" N ILE C1233 " pdb=" CA ILE C1233 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N VAL C1465 " pdb=" CA VAL C1465 " ideal model delta sigma weight residual 1.462 1.495 -0.032 9.10e-03 1.21e+04 1.27e+01 ... (remaining 14194 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.66: 458 105.66 - 112.83: 7271 112.83 - 120.01: 6236 120.01 - 127.19: 5260 127.19 - 134.36: 72 Bond angle restraints: 19297 Sorted by residual: angle pdb=" CA GLY A 382 " pdb=" C GLY A 382 " pdb=" O GLY A 382 " ideal model delta sigma weight residual 122.37 117.89 4.48 7.30e-01 1.88e+00 3.77e+01 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 122.23 118.25 3.98 6.90e-01 2.10e+00 3.33e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" O GLY A 377 " ideal model delta sigma weight residual 122.22 118.57 3.65 6.50e-01 2.37e+00 3.15e+01 angle pdb=" CA GLY D 82A" pdb=" C GLY D 82A" pdb=" O GLY D 82A" ideal model delta sigma weight residual 121.47 116.51 4.96 9.00e-01 1.23e+00 3.04e+01 angle pdb=" N PRO A 117 " pdb=" CA PRO A 117 " pdb=" C PRO A 117 " ideal model delta sigma weight residual 113.40 120.29 -6.89 1.34e+00 5.57e-01 2.64e+01 ... (remaining 19292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8601 21.75 - 43.50: 271 43.50 - 65.24: 43 65.24 - 86.99: 43 86.99 - 108.74: 30 Dihedral angle restraints: 8988 sinusoidal: 3978 harmonic: 5010 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -175.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 481 " pdb=" CB CYS A 481 " ideal model delta sinusoidal sigma weight residual 93.00 174.80 -81.80 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual -86.00 -28.05 -57.95 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 8985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1691 0.127 - 0.254: 535 0.254 - 0.382: 11 0.382 - 0.509: 1 0.509 - 0.636: 3 Chirality restraints: 2241 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.76 0.64 2.00e-02 2.50e+03 1.01e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.52e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.06e+02 ... (remaining 2238 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG F 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.110 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.352 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG H 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG O 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.157 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.515 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.104 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 57 2.41 - 3.03: 8774 3.03 - 3.66: 19318 3.66 - 4.28: 28927 4.28 - 4.90: 49145 Nonbonded interactions: 106221 Sorted by model distance: nonbonded pdb=" OD1 ASN B 224 " pdb="MN MN B 803 " model vdw 1.790 2.320 nonbonded pdb=" O TYR A 430 " pdb="MN MN A1104 " model vdw 1.812 2.320 nonbonded pdb=" OD1 ASP A 247 " pdb="MN MN A1101 " model vdw 1.843 2.320 nonbonded pdb=" O LEU A 257 " pdb=" OG1 THR A 258 " model vdw 1.907 2.440 nonbonded pdb=" OD1 ASN A 428 " pdb="MN MN A1104 " model vdw 1.930 2.320 ... (remaining 106216 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 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'L' selection = chain 'O' } 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=0.50 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.950 Check model and map are aligned: 0.180 Set scattering table: 0.150 Process input model: 41.570 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.048 14199 Z= 0.897 Angle : 1.475 8.603 19297 Z= 1.111 Chirality : 0.110 0.636 2241 Planarity : 0.020 0.306 2476 Dihedral : 14.023 108.740 5749 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 40.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Rotamer: Outliers : 0.93 % Allowed : 6.87 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.97 (0.19), residues: 1737 helix: 2.61 (0.38), residues: 196 sheet: 1.75 (0.22), residues: 536 loop : -0.40 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1164 HIS 0.004 0.001 HIS E 34 PHE 0.016 0.001 PHE A 285 TYR 0.015 0.001 TYR A 208 ARG 0.004 0.000 ARG C1374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8331 (pt) REVERT: C 1262 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6178 (mm) REVERT: D 12 VAL cc_start: 0.5524 (t) cc_final: 0.4067 (p) REVERT: D 119 PHE cc_start: 0.5956 (t80) cc_final: 0.5430 (t80) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.3216 time to fit residues: 96.3975 Evaluate side-chains 102 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1262 ILE Chi-restraints excluded: chain D residue 117 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 51 GLN A 161 GLN A 191 GLN A 218 GLN A 329 GLN A 380 GLN A 510 GLN B 201 ASN B 286 ASN ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN B 413 ASN C1183 ASN C1198 GLN C1205 ASN C1296 ASN C1323 GLN C1457 ASN C1461 GLN D 76 ASN D 81 GLN E 136 GLN E 150 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14199 Z= 0.283 Angle : 0.811 16.774 19297 Z= 0.392 Chirality : 0.052 0.427 2241 Planarity : 0.005 0.047 2476 Dihedral : 11.877 85.549 2581 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.47 % Allowed : 8.87 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 1.09 (0.20), residues: 1737 helix: 2.07 (0.33), residues: 219 sheet: 1.46 (0.21), residues: 607 loop : -0.10 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 118 HIS 0.005 0.001 HIS B 282 PHE 0.026 0.002 PHE D 67 TYR 0.024 0.002 TYR C1488 ARG 0.009 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.7826 (mmt) cc_final: 0.7568 (mmp) REVERT: B 236 MET cc_start: 0.6541 (tpp) cc_final: 0.6335 (tpp) REVERT: C 1262 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6376 (mm) REVERT: D 137 PRO cc_start: 0.8823 (Cg_exo) cc_final: 0.8551 (Cg_endo) REVERT: E 139 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: E 144 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8326 (tmtt) outliers start: 37 outliers final: 18 residues processed: 137 average time/residue: 0.3076 time to fit residues: 60.4793 Evaluate side-chains 104 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1262 ILE Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1413 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14199 Z= 0.325 Angle : 0.752 12.454 19297 Z= 0.373 Chirality : 0.049 0.244 2241 Planarity : 0.005 0.050 2476 Dihedral : 9.513 79.180 2575 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 10.67 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.82 (0.20), residues: 1737 helix: 1.59 (0.34), residues: 211 sheet: 1.28 (0.21), residues: 594 loop : -0.16 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 118 HIS 0.005 0.001 HIS A 345 PHE 0.026 0.003 PHE B 264 TYR 0.026 0.002 TYR D 117 ARG 0.012 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 87 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 546 MET cc_start: 0.7986 (mmt) cc_final: 0.7696 (mmp) REVERT: B 102 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6235 (mtm110) REVERT: B 236 MET cc_start: 0.7376 (tpp) cc_final: 0.6948 (tpp) REVERT: D 0 MET cc_start: 0.5141 (tpt) cc_final: 0.4881 (tpt) REVERT: D 100 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6325 (t80) REVERT: E 139 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: E 159 LYS cc_start: 0.7548 (mmtt) cc_final: 0.6892 (mptt) outliers start: 39 outliers final: 18 residues processed: 119 average time/residue: 0.3119 time to fit residues: 52.8217 Evaluate side-chains 95 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 121 TYR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1450 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 0.0670 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 161 GLN A 191 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14199 Z= 0.229 Angle : 0.646 11.888 19297 Z= 0.317 Chirality : 0.047 0.317 2241 Planarity : 0.004 0.053 2476 Dihedral : 8.464 72.799 2573 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 12.00 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.90 (0.20), residues: 1737 helix: 1.71 (0.35), residues: 214 sheet: 1.11 (0.21), residues: 612 loop : 0.03 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 118 HIS 0.004 0.001 HIS B 292 PHE 0.020 0.002 PHE D 67 TYR 0.026 0.002 TYR D 117 ARG 0.010 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8204 (t80) REVERT: B 82 THR cc_start: 0.3120 (OUTLIER) cc_final: 0.2912 (p) REVERT: B 102 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6408 (mtm110) REVERT: D 0 MET cc_start: 0.5178 (tpt) cc_final: 0.4916 (tpt) REVERT: D 100 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6335 (t80) REVERT: E 152 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 159 LYS cc_start: 0.7430 (mmtt) cc_final: 0.6799 (mttm) outliers start: 36 outliers final: 20 residues processed: 106 average time/residue: 0.2840 time to fit residues: 43.9657 Evaluate side-chains 97 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 191 GLN B 11 ASN B 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14199 Z= 0.231 Angle : 0.620 9.786 19297 Z= 0.308 Chirality : 0.046 0.259 2241 Planarity : 0.004 0.041 2476 Dihedral : 8.326 72.542 2571 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.33 % Allowed : 12.80 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.89 (0.20), residues: 1737 helix: 1.75 (0.35), residues: 213 sheet: 1.11 (0.21), residues: 606 loop : 0.01 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 118 HIS 0.010 0.001 HIS B 301 PHE 0.016 0.002 PHE B 264 TYR 0.030 0.002 TYR E 145 ARG 0.008 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 76 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 546 MET cc_start: 0.8211 (mmm) cc_final: 0.7943 (mmp) REVERT: B 82 THR cc_start: 0.3154 (OUTLIER) cc_final: 0.2916 (p) REVERT: D 0 MET cc_start: 0.5220 (tpt) cc_final: 0.4982 (tpt) REVERT: D 100 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.6768 (t80) REVERT: D 142 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8136 (mt-10) REVERT: E 159 LYS cc_start: 0.7521 (mmtt) cc_final: 0.6884 (mttm) outliers start: 35 outliers final: 19 residues processed: 109 average time/residue: 0.2960 time to fit residues: 46.6496 Evaluate side-chains 91 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14199 Z= 0.309 Angle : 0.680 9.874 19297 Z= 0.343 Chirality : 0.048 0.301 2241 Planarity : 0.005 0.041 2476 Dihedral : 8.168 67.842 2571 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.33 % Allowed : 13.47 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.69 (0.20), residues: 1737 helix: 1.54 (0.35), residues: 214 sheet: 0.93 (0.20), residues: 619 loop : -0.08 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 123 HIS 0.005 0.001 HIS B 292 PHE 0.023 0.002 PHE B 264 TYR 0.030 0.002 TYR E 145 ARG 0.020 0.001 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 75 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 546 MET cc_start: 0.8270 (mmm) cc_final: 0.7943 (mmp) REVERT: B 38 MET cc_start: 0.5112 (mmm) cc_final: 0.4081 (ptm) REVERT: B 82 THR cc_start: 0.3308 (OUTLIER) cc_final: 0.3064 (p) REVERT: D 0 MET cc_start: 0.5855 (tpt) cc_final: 0.5509 (tpt) REVERT: D 100 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6650 (t80) REVERT: D 142 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 159 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7058 (mttm) outliers start: 35 outliers final: 28 residues processed: 109 average time/residue: 0.2690 time to fit residues: 44.1379 Evaluate side-chains 99 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 68 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1339 THR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1394 VAL Chi-restraints excluded: chain C residue 1398 VAL Chi-restraints excluded: chain C residue 1416 VAL Chi-restraints excluded: chain C residue 1429 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 70.8175 > 50: distance: 0 - 6: 56.836 distance: 1 - 2: 40.091 distance: 1 - 4: 40.863 distance: 2 - 3: 40.971 distance: 2 - 7: 55.958 distance: 5 - 6: 39.582 distance: 7 - 8: 41.352 distance: 8 - 9: 57.486 distance: 8 - 11: 40.186 distance: 9 - 10: 55.396 distance: 11 - 12: 40.825 distance: 12 - 13: 40.681 distance: 15 - 16: 40.226 distance: 16 - 17: 55.844 distance: 16 - 19: 40.970 distance: 17 - 18: 8.171 distance: 17 - 21: 57.546 distance: 21 - 22: 40.853 distance: 21 - 27: 11.260 distance: 22 - 23: 56.570 distance: 22 - 25: 55.218 distance: 23 - 28: 56.889 distance: 26 - 27: 38.524 distance: 28 - 34: 39.202 distance: 30 - 35: 57.582 distance: 33 - 34: 39.005 distance: 36 - 39: 39.079 distance: 37 - 38: 39.459 distance: 37 - 42: 40.229 distance: 39 - 40: 39.334 distance: 39 - 41: 40.926 distance: 42 - 43: 56.560 distance: 43 - 44: 40.005 distance: 44 - 50: 41.191 distance: 47 - 49: 40.214 distance: 50 - 51: 39.495 distance: 51 - 52: 41.431 distance: 51 - 54: 40.125 distance: 52 - 53: 38.999 distance: 52 - 58: 39.911 distance: 55 - 57: 39.914 distance: 58 - 59: 40.433 distance: 58 - 88: 31.898 distance: 59 - 60: 39.233 distance: 59 - 62: 39.732 distance: 60 - 68: 34.170 distance: 61 - 85: 35.070 distance: 62 - 63: 41.061 distance: 63 - 64: 69.261 distance: 63 - 65: 55.299 distance: 64 - 66: 40.433 distance: 66 - 67: 55.624