Starting phenix.real_space_refine (version: dev) on Tue Dec 13 11:30:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/12_2022/6hup_0283_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "G PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15265 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "K" 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: 3 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'ABU': 1, 'DZP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'DZP': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'ABU': 1, 'DZP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.52, per 1000 atoms: 0.56 Number of scatterers: 15265 At special positions: 0 Unit cell: (99.345, 122.615, 135.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 83 16.00 P 6 15.00 O 2818 8.00 N 2477 7.00 C 9878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.05 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.02 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " distance=2.02 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 F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 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 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-ASN " NAG F 1 " - " ASN A 111 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 111 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 2.3 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 31.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 246 removed outlier: 4.736A pdb=" N LEU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 5.339A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 274 Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.548A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.306A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.852A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.044A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.865A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 445 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.337A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.848A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 321 Processing helix chain 'C' and resid 407 through 434 removed outlier: 5.133A pdb=" N ASP C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 413 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 415 " --> pdb=" O SER C 412 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE C 418 " --> pdb=" O ARG C 415 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.539A pdb=" N PHE C 422 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 429 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 432 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 433 " --> pdb=" O TRP C 430 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.128A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 5.083A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 4.069A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 414 Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.570A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 4.079A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 Processing helix chain 'E' and resid 280 through 307 removed outlier: 3.547A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 4.034A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'G' and resid 493 through 495 No H-bonds generated for 'chain 'G' and resid 493 through 495' Processing sheet with id= A, first strand: chain 'A' and resid 39 through 43 Processing sheet with id= B, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.782A pdb=" N SER A 49 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE A 65 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 47 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG A 67 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE A 45 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.163A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.754A pdb=" N HIS A 218 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.337A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 127 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.507A pdb=" N GLN B 148 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 211 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.711A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 142 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.798A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.581A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.066A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 69 through 71 Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'D' and resid 150 through 154 Processing sheet with id= O, first strand: chain 'D' and resid 196 through 204 Processing sheet with id= P, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.318A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= R, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= S, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.723A pdb=" N GLN G 5 " --> pdb=" O ALA G 429 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 498 through 502 removed outlier: 3.576A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1737 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: 4.39 Time building geometry restraints manager: 7.01 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: 2818 1.32 - 1.45: 4347 1.45 - 1.57: 8330 1.57 - 1.69: 10 1.69 - 1.82: 146 Bond restraints: 15651 Sorted by residual: bond pdb=" CB THR C 215 " pdb=" CG2 THR C 215 " ideal model delta sigma weight residual 1.521 1.383 0.138 3.30e-02 9.18e+02 1.74e+01 bond pdb=" O4 PIO D2002 " pdb=" P4 PIO D2002 " ideal model delta sigma weight residual 1.648 1.574 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 1.648 1.579 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1B PIO D2002 " pdb=" O3C PIO D2002 " ideal model delta sigma weight residual 1.398 1.332 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 1.648 1.582 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 15646 not shown) Histogram of bond angle deviations from ideal: 94.76 - 102.99: 122 102.99 - 111.22: 6541 111.22 - 119.45: 6570 119.45 - 127.68: 7878 127.68 - 135.91: 159 Bond angle restraints: 21270 Sorted by residual: angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 113.43 101.90 11.53 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 108.85 124.03 -15.18 1.54e+00 4.22e-01 9.72e+01 angle pdb=" N ALA G 505 " pdb=" CA ALA G 505 " pdb=" C ALA G 505 " ideal model delta sigma weight residual 108.41 94.76 13.65 1.63e+00 3.76e-01 7.01e+01 angle pdb=" N TRP G 508 " pdb=" CA TRP G 508 " pdb=" C TRP G 508 " ideal model delta sigma weight residual 111.39 100.13 11.26 1.38e+00 5.25e-01 6.66e+01 angle pdb=" N ASP B 146 " pdb=" CA ASP B 146 " pdb=" C ASP B 146 " ideal model delta sigma weight residual 110.48 119.42 -8.94 1.48e+00 4.57e-01 3.65e+01 ... (remaining 21265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 8753 16.14 - 32.29: 334 32.29 - 48.43: 40 48.43 - 64.57: 11 64.57 - 80.72: 1 Dihedral angle restraints: 9139 sinusoidal: 3817 harmonic: 5322 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 146.85 -53.85 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ASN B 80 " pdb=" CA ASN B 80 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP E 30 " pdb=" C ASP E 30 " pdb=" N PHE E 31 " pdb=" CA PHE E 31 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 9136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2407 0.185 - 0.370: 56 0.370 - 0.555: 1 0.555 - 0.740: 1 0.740 - 0.925: 2 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C1 MAN I 4 " pdb=" O6 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.14e+03 chirality pdb=" C1 MAN I 6 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 6 " pdb=" O5 MAN I 6 " both_signs ideal model delta sigma weight residual False 2.40 1.78 0.62 2.00e-02 2.50e+03 9.58e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 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 2464 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.261 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C7 NAG I 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.366 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 DZP B 502 " -0.035 2.00e-02 2.50e+03 4.91e-02 5.43e+01 pdb=" C14 DZP B 502 " -0.034 2.00e-02 2.50e+03 pdb=" C5 DZP B 502 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DZP B 502 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DZP B 502 " -0.042 2.00e-02 2.50e+03 pdb=" C9 DZP B 502 " -0.027 2.00e-02 2.50e+03 pdb=" CL DZP B 502 " 0.090 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP B 502 " -0.046 2.00e-02 2.50e+03 5.27e-02 4.16e+01 pdb=" C18 DZP B 502 " -0.022 2.00e-02 2.50e+03 pdb=" C20 DZP B 502 " -0.042 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " 0.072 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " -0.038 2.00e-02 2.50e+03 pdb=" O1 DZP B 502 " 0.075 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3552 2.78 - 3.31: 13377 3.31 - 3.84: 25940 3.84 - 4.37: 30444 4.37 - 4.90: 52426 Nonbonded interactions: 125739 Sorted by model distance: nonbonded pdb=" OH TYR E 57 " pdb=" O THR E 151 " model vdw 2.251 2.440 nonbonded pdb=" O THR B 233 " pdb=" OG SER B 236 " model vdw 2.275 2.440 nonbonded pdb=" O SER D 244 " pdb=" NH1 ARG D 255 " model vdw 2.292 2.520 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.295 2.440 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.301 2.440 ... (remaining 125734 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 'A' and (resid 13 through 320 or resid 384 through 418)) selection = (chain 'D' and resid 13 through 418) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447 or resid 501 throug \ h 502)) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 83 5.16 5 Cl 3 4.86 5 C 9878 2.51 5 N 2477 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.050 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.140 Process input model: 40.050 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 0.138 15651 Z= 0.864 Angle : 1.180 15.183 21270 Z= 0.658 Chirality : 0.078 0.925 2467 Planarity : 0.010 0.218 2582 Dihedral : 8.913 80.716 5699 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.17), residues: 1784 helix: -1.65 (0.17), residues: 561 sheet: -2.32 (0.22), residues: 459 loop : -2.59 (0.19), residues: 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.3151 time to fit residues: 230.3250 Evaluate side-chains 294 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 189 ASN A 216 HIS B 64 GLN B 224 GLN B 265 ASN C 80 GLN C 156 HIS C 182 GLN C 239 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN G 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15651 Z= 0.214 Angle : 0.630 10.343 21270 Z= 0.335 Chirality : 0.044 0.327 2467 Planarity : 0.005 0.054 2582 Dihedral : 6.891 59.879 2306 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -2.03 (0.19), residues: 1784 helix: 0.14 (0.21), residues: 556 sheet: -1.90 (0.22), residues: 478 loop : -2.03 (0.20), residues: 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 334 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 27 residues processed: 362 average time/residue: 0.2871 time to fit residues: 150.0453 Evaluate side-chains 308 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1630 time to fit residues: 10.1662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.0870 chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 175 optimal weight: 0.0970 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN B 224 GLN B 265 ASN C 154 GLN C 318 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15651 Z= 0.157 Angle : 0.552 8.784 21270 Z= 0.290 Chirality : 0.042 0.309 2467 Planarity : 0.004 0.046 2582 Dihedral : 6.236 57.686 2306 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.34 (0.19), residues: 1784 helix: 0.89 (0.22), residues: 551 sheet: -1.56 (0.23), residues: 476 loop : -1.73 (0.21), residues: 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 319 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 333 average time/residue: 0.2858 time to fit residues: 137.9608 Evaluate side-chains 303 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 288 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1613 time to fit residues: 6.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN G 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15651 Z= 0.189 Angle : 0.543 8.663 21270 Z= 0.282 Chirality : 0.042 0.294 2467 Planarity : 0.004 0.045 2582 Dihedral : 5.962 58.444 2306 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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 (0.20), residues: 1784 helix: 1.22 (0.23), residues: 558 sheet: -1.37 (0.23), residues: 475 loop : -1.53 (0.22), residues: 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 297 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 314 average time/residue: 0.2843 time to fit residues: 130.0788 Evaluate side-chains 281 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 263 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1582 time to fit residues: 7.4292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 chunk 119 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS C 154 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN G 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15651 Z= 0.164 Angle : 0.520 8.179 21270 Z= 0.270 Chirality : 0.042 0.287 2467 Planarity : 0.004 0.046 2582 Dihedral : 5.775 59.310 2306 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.75 (0.20), residues: 1784 helix: 1.41 (0.23), residues: 558 sheet: -1.30 (0.23), residues: 488 loop : -1.35 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 310 average time/residue: 0.2617 time to fit residues: 120.5141 Evaluate side-chains 287 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1477 time to fit residues: 6.5800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN D 204 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15651 Z= 0.190 Angle : 0.529 7.907 21270 Z= 0.273 Chirality : 0.042 0.280 2467 Planarity : 0.004 0.049 2582 Dihedral : 5.653 56.201 2306 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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 (0.20), residues: 1784 helix: 1.57 (0.23), residues: 557 sheet: -1.14 (0.23), residues: 488 loop : -1.34 (0.23), residues: 739 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 281 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 293 average time/residue: 0.2710 time to fit residues: 117.8216 Evaluate side-chains 270 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 261 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1427 time to fit residues: 4.7564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN D 242 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15651 Z= 0.213 Angle : 0.551 10.083 21270 Z= 0.280 Chirality : 0.042 0.279 2467 Planarity : 0.004 0.047 2582 Dihedral : 5.613 51.403 2306 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.48 (0.20), residues: 1784 helix: 1.58 (0.23), residues: 559 sheet: -1.08 (0.23), residues: 476 loop : -1.22 (0.23), residues: 749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 280 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 292 average time/residue: 0.2606 time to fit residues: 113.7804 Evaluate side-chains 270 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1325 time to fit residues: 4.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN C 156 HIS D 242 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15651 Z= 0.284 Angle : 0.576 9.160 21270 Z= 0.298 Chirality : 0.043 0.278 2467 Planarity : 0.004 0.066 2582 Dihedral : 5.720 51.218 2306 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.48 (0.20), residues: 1784 helix: 1.57 (0.23), residues: 558 sheet: -1.07 (0.23), residues: 486 loop : -1.19 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 1.885 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 269 average time/residue: 0.2701 time to fit residues: 108.8905 Evaluate side-chains 260 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 247 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1722 time to fit residues: 6.2775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 0.0770 chunk 145 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15651 Z= 0.168 Angle : 0.544 9.808 21270 Z= 0.277 Chirality : 0.042 0.265 2467 Planarity : 0.004 0.052 2582 Dihedral : 5.582 52.137 2306 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.42 (0.20), residues: 1784 helix: 1.64 (0.23), residues: 558 sheet: -1.12 (0.23), residues: 486 loop : -1.12 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 1.959 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 287 average time/residue: 0.2708 time to fit residues: 116.9977 Evaluate side-chains 267 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1525 time to fit residues: 3.2941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN C 54 HIS E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15651 Z= 0.216 Angle : 0.568 10.933 21270 Z= 0.288 Chirality : 0.042 0.269 2467 Planarity : 0.004 0.051 2582 Dihedral : 5.582 56.414 2306 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.37 (0.20), residues: 1784 helix: 1.68 (0.23), residues: 557 sheet: -1.08 (0.23), residues: 488 loop : -1.08 (0.23), residues: 739 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 1.798 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 265 average time/residue: 0.2782 time to fit residues: 111.8766 Evaluate side-chains 260 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 254 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1726 time to fit residues: 4.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 0.0030 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092676 restraints weight = 27941.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095751 restraints weight = 13688.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097759 restraints weight = 8689.921| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15651 Z= 0.215 Angle : 0.570 10.949 21270 Z= 0.288 Chirality : 0.042 0.266 2467 Planarity : 0.004 0.050 2582 Dihedral : 5.576 57.270 2306 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1784 helix: 1.71 (0.23), residues: 558 sheet: -1.06 (0.23), residues: 491 loop : -1.09 (0.23), residues: 735 =============================================================================== Job complete usr+sys time: 3285.97 seconds wall clock time: 60 minutes 27.41 seconds (3627.41 seconds total)