Starting phenix.real_space_refine (version: dev) on Tue Feb 21 16:08:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huj_0279/02_2023/6huj_0279_updated.pdb" } resolution = 3.04 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= 0.007 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 Process input model Symmetric amino acids flipped Residue "A ARG 21": "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 85": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 187": "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 TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15255 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2809 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} 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: 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: "I" 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: "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: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'ABU': 1, 'PIO': 1, 'RI5': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ABU': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.65, per 1000 atoms: 0.57 Number of scatterers: 15255 At special positions: 0 Unit cell: (100.58, 120.91, 135.89, 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) S 83 16.00 P 6 15.00 O 2830 8.00 N 2476 7.00 C 9860 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=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.04 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " distance=2.03 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 H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 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 H 3 " - " MAN H 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " 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 149 " " NAG I 1 " - " ASN B 80 " " 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: 6.55 Conformation dependent library (CDL) restraints added in 2.3 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 31.7% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 3.936A pdb=" N THR A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) 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 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' 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 229 removed outlier: 3.747A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 5.003A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.535A pdb=" N THR A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.556A pdb=" N VAL A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 3.623A pdb=" N SER A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.955A 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 9 through 19 removed outlier: 3.541A pdb=" N THR B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.511A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.586A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.541A pdb=" N THR B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 4.130A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 306 removed outlier: 3.583A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 removed outlier: 3.610A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.536A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 234 through 239 removed outlier: 4.007A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 3.530A pdb=" N VAL C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 4.192A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 295 through 321 removed outlier: 3.802A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 432 removed outlier: 4.074A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.653A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 20 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 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 224 through 229 removed outlier: 4.012A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.086A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 272 removed outlier: 3.501A pdb=" N THR D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 3.555A pdb=" N VAL D 292 " --> pdb=" O TRP D 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 297 " --> pdb=" O CYS D 293 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 414 removed outlier: 4.057A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 3.566A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 19 removed outlier: 3.598A pdb=" N GLU E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) 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: 3.530A 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 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 4.018A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN E 224 " --> pdb=" O TYR E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 219 through 224' Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.683A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 269 removed outlier: 3.679A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 307 removed outlier: 3.605A pdb=" N TYR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 4.057A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE E 431 " --> pdb=" O SER E 427 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.638A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 495 No H-bonds generated for 'chain 'G' and resid 493 through 495' Processing helix chain 'G' and resid 513 through 515 No H-bonds generated for 'chain 'G' and resid 513 through 515' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.766A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.145A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.258A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.715A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 186 through 188 Processing sheet with id= G, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.709A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.070A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= J, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.729A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.671A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.352A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) 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 196 through 205 Processing sheet with id= O, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.358A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 127 " --> pdb=" O MET E 115 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.685A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= R, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.741A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.574A pdb=" N SER G 476 " --> pdb=" O ASP G 485 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 501 through 504 removed outlier: 3.502A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1644 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: 4.52 Time building geometry restraints manager: 7.07 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: 2344 1.32 - 1.44: 4659 1.44 - 1.57: 8483 1.57 - 1.69: 10 1.69 - 1.81: 143 Bond restraints: 15639 Sorted by residual: bond pdb=" C1B PIO A 508 " pdb=" O3C PIO A 508 " ideal model delta sigma weight residual 1.399 1.333 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1B PIO D 506 " pdb=" O3C PIO D 506 " ideal model delta sigma weight residual 1.399 1.335 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2C PIO D 506 " pdb=" O2C PIO D 506 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C2C PIO A 508 " pdb=" O2C PIO A 508 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" O13 PIO A 508 " pdb=" P1 PIO A 508 " ideal model delta sigma weight residual 1.648 1.589 0.059 2.00e-02 2.50e+03 8.80e+00 ... (remaining 15634 not shown) Histogram of bond angle deviations from ideal: 59.24 - 74.87: 3 74.87 - 90.50: 0 90.50 - 106.12: 363 106.12 - 121.75: 17447 121.75 - 137.38: 3451 Bond angle restraints: 21264 Sorted by residual: angle pdb=" C2 NAG M 1 " pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 109.64 114.40 -4.76 5.38e-01 3.45e+00 7.83e+01 angle pdb=" N VAL D 389 " pdb=" CA VAL D 389 " pdb=" C VAL D 389 " ideal model delta sigma weight residual 112.29 107.12 5.17 9.40e-01 1.13e+00 3.02e+01 angle pdb=" N VAL B 124 " pdb=" CA VAL B 124 " pdb=" C VAL B 124 " ideal model delta sigma weight residual 108.12 114.92 -6.80 1.44e+00 4.82e-01 2.23e+01 angle pdb=" N VAL E 124 " pdb=" CA VAL E 124 " pdb=" C VAL E 124 " ideal model delta sigma weight residual 108.12 114.91 -6.79 1.44e+00 4.82e-01 2.23e+01 angle pdb=" C2 NAG L 2 " pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 109.64 112.08 -2.44 5.38e-01 3.45e+00 2.05e+01 ... (remaining 21259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 8889 17.08 - 34.16: 223 34.16 - 51.25: 39 51.25 - 68.33: 6 68.33 - 85.41: 4 Dihedral angle restraints: 9161 sinusoidal: 3827 harmonic: 5334 Sorted by residual: dihedral pdb=" CA PRO D 154 " pdb=" C PRO D 154 " pdb=" N LEU D 155 " pdb=" CA LEU D 155 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS C 151 " pdb=" SG CYS C 151 " pdb=" SG CYS C 165 " pdb=" CB CYS C 165 " ideal model delta sinusoidal sigma weight residual 93.00 52.57 40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 9158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 2473 0.254 - 0.508: 6 0.508 - 0.762: 0 0.762 - 1.016: 0 1.016 - 1.270: 1 Chirality restraints: 2480 Sorted by residual: chirality pdb=" C1 MAN F 5 " pdb=" O3 MAN F 4 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 MAN H 5 " pdb=" O3 MAN H 4 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.73e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.55e+02 ... (remaining 2477 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.210 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" C7 NAG K 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.285 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.209 2.00e-02 2.50e+03 1.74e-01 3.78e+02 pdb=" C7 NAG L 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.285 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.120 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C7 NAG M 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.163 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.017 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3748 2.79 - 3.32: 12821 3.32 - 3.85: 25561 3.85 - 4.37: 31133 4.37 - 4.90: 52948 Nonbonded interactions: 126211 Sorted by model distance: nonbonded pdb=" OG1 THR D 163 " pdb=" OE1 GLU D 166 " model vdw 2.265 2.440 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.286 2.440 nonbonded pdb=" OD1 ASP A 55 " pdb=" OH TYR A 191 " model vdw 2.304 2.440 nonbonded pdb=" OE1 GLN B 64 " pdb=" OH TYR B 66 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASP E 101 " pdb=" OG1 THR E 132 " model vdw 2.311 2.440 ... (remaining 126206 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 12 through 320 or resid 384 through 418 or resid 508)) selection = (chain 'D' and (resid 12 through 418 or (resid 506 and (name C1 or name C1A or n \ ame C1B or name C1C or name C2 or name C2A or name C2B or name C2C or name C3 or \ name C3A or name C3B or name C3C or name C4 or name C4A or name C4B or name C5 \ or name C5A or name C5B or name C6 or name C6A or name C6B or name C7A or name C \ 7B or name C8B or name O1 or name O11 or name O12 or name O13 or name O1A or nam \ e O1B or name O2 or name O2C or name O3 or name O3C or name O4 or name O41 or na \ me O42 or name O43 or name O5 or name O51 or name O52 or name O53 or name O6 or \ name P1 or name P4 or name P5 )))) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447)) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'H' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'I' 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 83 5.16 5 C 9860 2.51 5 N 2476 2.21 5 O 2830 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.920 Check model and map are aligned: 0.230 Process input model: 40.510 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 15639 Z= 0.354 Angle : 0.860 13.325 21264 Z= 0.462 Chirality : 0.061 1.270 2480 Planarity : 0.009 0.174 2582 Dihedral : 8.709 85.412 5713 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -4.37 (0.16), residues: 1788 helix: -4.22 (0.09), residues: 530 sheet: -2.02 (0.21), residues: 479 loop : -2.28 (0.19), residues: 779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.3907 time to fit residues: 221.8695 Evaluate side-chains 247 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5834 ------------------------------------------------------------------------------- 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: 0.7980 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 54 ASN B 224 GLN C 152 GLN C 323 ASN D 308 ASN E 54 ASN E 100 ASN E 224 GLN E 267 HIS E 303 ASN G 445 GLN G 463 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 15639 Z= 0.294 Angle : 0.596 9.110 21264 Z= 0.315 Chirality : 0.044 0.335 2480 Planarity : 0.005 0.050 2582 Dihedral : 6.347 78.811 2314 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.73 % 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: -2.51 (0.18), residues: 1788 helix: -1.73 (0.17), residues: 540 sheet: -1.33 (0.22), residues: 473 loop : -1.66 (0.22), residues: 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 268 average time/residue: 0.2907 time to fit residues: 112.6215 Evaluate side-chains 247 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1553 time to fit residues: 8.2736 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 224 GLN C 80 GLN C 152 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15639 Z= 0.228 Angle : 0.534 9.049 21264 Z= 0.279 Chirality : 0.043 0.335 2480 Planarity : 0.004 0.041 2582 Dihedral : 6.063 83.936 2314 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.49 % 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: -1.42 (0.19), residues: 1788 helix: -0.09 (0.21), residues: 535 sheet: -1.04 (0.23), residues: 470 loop : -1.37 (0.22), residues: 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 237 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 253 average time/residue: 0.3061 time to fit residues: 110.6123 Evaluate side-chains 240 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1382 time to fit residues: 5.1149 ------------------------------------------------------------------------------- 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: 4.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 152 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15639 Z= 0.207 Angle : 0.517 8.656 21264 Z= 0.268 Chirality : 0.042 0.332 2480 Planarity : 0.004 0.037 2582 Dihedral : 5.920 82.772 2314 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.24 % 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: -0.84 (0.20), residues: 1788 helix: 0.73 (0.22), residues: 539 sheet: -0.87 (0.23), residues: 472 loop : -1.20 (0.23), residues: 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 245 average time/residue: 0.3041 time to fit residues: 107.8223 Evaluate side-chains 240 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1653 time to fit residues: 6.5528 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 147 optimal weight: 0.0870 chunk 119 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 224 GLN C 152 GLN E 54 ASN E 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 15639 Z= 0.168 Angle : 0.493 8.806 21264 Z= 0.255 Chirality : 0.041 0.330 2480 Planarity : 0.004 0.038 2582 Dihedral : 5.816 80.648 2314 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.99 % 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: -0.53 (0.20), residues: 1788 helix: 1.11 (0.22), residues: 542 sheet: -0.71 (0.24), residues: 466 loop : -1.11 (0.23), residues: 780 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 246 average time/residue: 0.3015 time to fit residues: 107.2435 Evaluate side-chains 237 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 1.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1341 time to fit residues: 4.5352 ------------------------------------------------------------------------------- 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: 0.9980 chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 173 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15639 Z= 0.187 Angle : 0.499 8.832 21264 Z= 0.257 Chirality : 0.042 0.330 2480 Planarity : 0.004 0.039 2582 Dihedral : 5.806 80.465 2314 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.18 % 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: 1788 helix: 1.30 (0.23), residues: 543 sheet: -0.64 (0.24), residues: 466 loop : -1.05 (0.23), residues: 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 230 average time/residue: 0.3020 time to fit residues: 100.8223 Evaluate side-chains 235 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 1.777 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1661 time to fit residues: 6.1404 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 224 GLN C 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15639 Z= 0.287 Angle : 0.546 9.640 21264 Z= 0.281 Chirality : 0.043 0.333 2480 Planarity : 0.004 0.039 2582 Dihedral : 5.875 80.098 2314 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.93 % 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: -0.31 (0.21), residues: 1788 helix: 1.34 (0.22), residues: 543 sheet: -0.62 (0.23), residues: 486 loop : -0.99 (0.24), residues: 759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 225 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 231 average time/residue: 0.3011 time to fit residues: 101.0888 Evaluate side-chains 226 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.731 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1401 time to fit residues: 4.7056 ------------------------------------------------------------------------------- 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: 1.9990 chunk 68 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 54 ASN C 152 GLN E 54 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15639 Z= 0.177 Angle : 0.495 9.175 21264 Z= 0.254 Chirality : 0.041 0.331 2480 Planarity : 0.004 0.039 2582 Dihedral : 5.667 78.401 2314 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.37 % 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: -0.14 (0.21), residues: 1788 helix: 1.58 (0.23), residues: 544 sheet: -0.59 (0.24), residues: 469 loop : -0.92 (0.24), residues: 775 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 227 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 228 average time/residue: 0.3193 time to fit residues: 105.3564 Evaluate side-chains 227 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.970 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3854 time to fit residues: 4.6524 ------------------------------------------------------------------------------- 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: 4.9990 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 54 ASN C 152 GLN D 387 ASN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15639 Z= 0.236 Angle : 0.522 9.610 21264 Z= 0.266 Chirality : 0.042 0.334 2480 Planarity : 0.004 0.040 2582 Dihedral : 5.674 76.772 2314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.87 % 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: -0.09 (0.21), residues: 1788 helix: 1.57 (0.23), residues: 545 sheet: -0.47 (0.23), residues: 478 loop : -0.92 (0.24), residues: 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 226 average time/residue: 0.3022 time to fit residues: 99.3544 Evaluate side-chains 228 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 1.674 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1360 time to fit residues: 5.1196 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN ** G 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15639 Z= 0.174 Angle : 0.496 9.384 21264 Z= 0.254 Chirality : 0.041 0.330 2480 Planarity : 0.003 0.041 2582 Dihedral : 5.549 74.840 2314 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.37 % 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: 0.00 (0.21), residues: 1788 helix: 1.72 (0.23), residues: 543 sheet: -0.51 (0.24), residues: 468 loop : -0.85 (0.24), residues: 777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 223 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 225 average time/residue: 0.3099 time to fit residues: 101.2400 Evaluate side-chains 222 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 1.810 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1362 time to fit residues: 3.2194 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN C 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095094 restraints weight = 21436.372| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.01 r_work: 0.2975 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15639 Z= 0.290 Angle : 0.542 9.940 21264 Z= 0.277 Chirality : 0.043 0.334 2480 Planarity : 0.004 0.040 2582 Dihedral : 5.684 73.533 2314 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.37 % 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: -0.11 (0.21), residues: 1788 helix: 1.55 (0.23), residues: 548 sheet: -0.61 (0.24), residues: 476 loop : -0.84 (0.24), residues: 764 =============================================================================== Job complete usr+sys time: 3407.59 seconds wall clock time: 62 minutes 33.96 seconds (3753.96 seconds total)