Starting phenix.real_space_refine on Sun Dec 10 17:45:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/12_2023/6huo_0282_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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 1 4.86 5 C 9847 2.51 5 N 2475 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15227 Number of models: 1 Model: "" Number of chains: 16 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: 6 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 dihedrals: 6 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: 6 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 dihedrals: 6 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: 6 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 dihedrals: 6 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: 6 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'08H': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.56 Number of scatterers: 15227 At special positions: 0 Unit cell: (100.58, 123.05, 136.96, 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 1 17.00 S 83 16.00 P 6 15.00 O 2815 8.00 N 2475 7.00 C 9847 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=2.03 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 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: 6.16 Conformation dependent library (CDL) restraints added in 2.8 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: 50 helices and 17 sheets defined 32.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 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 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.574A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 252 through 274 removed outlier: 3.589A pdb=" N THR A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.519A pdb=" N PHE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 4.029A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.511A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 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 90 Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.832A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.107A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.831A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 removed outlier: 3.887A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.502A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 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 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.837A pdb=" N THR C 237 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.401A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 286 removed outlier: 3.601A pdb=" N THR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 321 removed outlier: 3.711A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 434 removed outlier: 4.071A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.637A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.512A pdb=" N ARG D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) 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 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.734A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.298A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.525A pdb=" N VAL D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 308 removed outlier: 3.759A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 414 removed outlier: 3.526A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 19 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 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 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.517A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 247 through 269 Processing helix chain 'E' and resid 280 through 306 removed outlier: 3.727A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 4.323A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.533A 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: 5.903A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (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: 4.085A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.614A 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: 6.183A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.756A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.836A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.874A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (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: 4.592A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.077A 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: 6.735A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.860A 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: 6.314A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 46 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 133 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 121 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 150 through 158 Processing sheet with id= M, first strand: chain 'D' and resid 196 through 205 Processing sheet with id= N, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.349A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 5 through 7 Processing sheet with id= Q, first strand: chain 'G' and resid 498 through 504 removed outlier: 3.789A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1713 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: 4.77 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2560 1.33 - 1.45: 4506 1.45 - 1.57: 8392 1.57 - 1.70: 8 1.70 - 1.82: 144 Bond restraints: 15610 Sorted by residual: bond pdb=" N PRO A 140 " pdb=" CD PRO A 140 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" C2C PIO D 502 " pdb=" O2C PIO D 502 " ideal model delta sigma weight residual 1.399 1.463 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1B PIO A 502 " pdb=" O3C PIO A 502 " ideal model delta sigma weight residual 1.399 1.336 0.063 2.00e-02 2.50e+03 9.97e+00 bond pdb=" C1B PIO D 502 " pdb=" O3C PIO D 502 " ideal model delta sigma weight residual 1.399 1.336 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" C2C PIO A 502 " pdb=" O2C PIO A 502 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.74e+00 ... (remaining 15605 not shown) Histogram of bond angle deviations from ideal: 92.74 - 100.99: 52 100.99 - 109.24: 1508 109.24 - 117.49: 9832 117.49 - 125.74: 9546 125.74 - 133.99: 275 Bond angle restraints: 21213 Sorted by residual: angle pdb=" N ALA G 505 " pdb=" CA ALA G 505 " pdb=" C ALA G 505 " ideal model delta sigma weight residual 108.52 92.74 15.78 1.63e+00 3.76e-01 9.37e+01 angle pdb=" C4 PIO D 502 " pdb=" O4 PIO D 502 " pdb=" P4 PIO D 502 " ideal model delta sigma weight residual 118.46 132.38 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C4 PIO A 502 " pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 118.46 132.08 -13.62 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C GLY G 509 " pdb=" N LEU G 510 " pdb=" CA LEU G 510 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C ASP C 192 " pdb=" N THR C 193 " pdb=" CA THR C 193 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 ... (remaining 21208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.28: 9132 28.28 - 56.56: 75 56.56 - 84.84: 8 84.84 - 113.12: 4 113.12 - 141.40: 3 Dihedral angle restraints: 9222 sinusoidal: 3900 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 93.00 161.60 -68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CA ALA B 280 " pdb=" C ALA B 280 " pdb=" N ILE B 281 " pdb=" CA ILE B 281 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+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 52.35 40.65 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 9219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 2446 0.205 - 0.411: 16 0.411 - 0.616: 3 0.616 - 0.821: 1 0.821 - 1.027: 1 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.37 1.03 2.00e-02 2.50e+03 2.64e+03 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.53e+02 chirality pdb=" C1 MAN M 5 " pdb=" O3 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.32e+02 ... (remaining 2464 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.039 2.00e-02 2.50e+03 3.25e-02 1.32e+01 pdb=" C7 NAG K 1 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 432 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 146 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO D 147 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 147 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 147 " -0.030 5.00e-02 4.00e+02 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3449 2.79 - 3.31: 12784 3.31 - 3.84: 25342 3.84 - 4.37: 30720 4.37 - 4.90: 52650 Nonbonded interactions: 124945 Sorted by model distance: nonbonded pdb=" OD1 ASP B 101 " pdb=" OG1 THR B 132 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR A 99 " pdb=" OH TYR A 169 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP D 98 " pdb=" OG SER D 159 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASP E 101 " pdb=" OG1 THR E 132 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR C 111 " pdb=" OH TYR C 181 " model vdw 2.304 2.440 ... (remaining 124940 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 or resid 502)) selection = (chain 'D' and (resid 13 through 418 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447)) selection = (chain 'E' and resid 8 through 447) } 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 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: 1.100 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: 4.200 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 43.340 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.006 0.064 15610 Z= 0.368 Angle : 0.886 15.779 21213 Z= 0.456 Chirality : 0.062 1.027 2467 Planarity : 0.007 0.063 2576 Dihedral : 9.667 141.400 5782 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -4.15 (0.15), residues: 1784 helix: -3.84 (0.10), residues: 558 sheet: -1.81 (0.21), residues: 487 loop : -2.29 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 95 HIS 0.012 0.002 HIS B 107 PHE 0.038 0.003 PHE C 113 TYR 0.021 0.002 TYR E 66 ARG 0.008 0.001 ARG A 249 *********************** 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 467 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.3770 time to fit residues: 241.1741 Evaluate side-chains 264 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2046 ------------------------------------------------------------------------------- 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: 2.9990 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 190 GLN A 308 ASN B 64 GLN B 185 GLN B 243 ASN C 66 ASN C 80 GLN C 99 ASN C 122 HIS C 157 ASN D 151 HIS D 189 ASN D 190 GLN D 417 ASN E 54 ASN E 65 GLN E 113 ASN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15610 Z= 0.358 Angle : 0.660 8.001 21213 Z= 0.348 Chirality : 0.046 0.228 2467 Planarity : 0.005 0.049 2576 Dihedral : 9.230 142.575 2389 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.04 % Allowed : 7.69 % Favored : 89.27 % 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: -2.11 (0.18), residues: 1784 helix: -0.86 (0.19), residues: 553 sheet: -1.39 (0.21), residues: 503 loop : -1.66 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 92 HIS 0.011 0.001 HIS G 517 PHE 0.027 0.002 PHE C 113 TYR 0.026 0.002 TYR D 309 ARG 0.007 0.001 ARG E 68 *********************** 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 314 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 265 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 35 residues processed: 299 average time/residue: 0.2860 time to fit residues: 124.6448 Evaluate side-chains 267 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1570 time to fit residues: 12.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2682 > 50: distance: 27 - 216: 36.205 distance: 30 - 213: 31.459 distance: 47 - 201: 32.602 distance: 50 - 198: 24.017 distance: 107 - 157: 34.726 distance: 110 - 154: 34.699 distance: 137 - 143: 32.699 distance: 143 - 144: 29.197 distance: 143 - 208: 11.398 distance: 144 - 145: 43.377 distance: 144 - 147: 24.101 distance: 145 - 146: 3.752 distance: 145 - 154: 36.856 distance: 146 - 205: 42.131 distance: 147 - 148: 20.102 distance: 148 - 149: 34.989 distance: 149 - 150: 21.602 distance: 150 - 151: 15.399 distance: 151 - 152: 9.957 distance: 151 - 153: 13.707 distance: 154 - 155: 26.240 distance: 155 - 156: 13.634 distance: 155 - 158: 10.811 distance: 156 - 157: 39.759 distance: 156 - 162: 22.438 distance: 158 - 159: 40.600 distance: 159 - 160: 26.323 distance: 159 - 161: 21.306 distance: 162 - 163: 22.053 distance: 163 - 164: 27.550 distance: 163 - 166: 27.007 distance: 164 - 165: 34.641 distance: 164 - 172: 35.718 distance: 166 - 167: 40.443 distance: 167 - 168: 55.604 distance: 167 - 169: 44.616 distance: 168 - 170: 41.299 distance: 169 - 171: 30.644 distance: 170 - 171: 33.167 distance: 172 - 173: 34.567 distance: 172 - 178: 33.291 distance: 173 - 176: 36.902 distance: 174 - 175: 39.597 distance: 177 - 178: 41.062 distance: 179 - 180: 4.297 distance: 180 - 181: 46.393 distance: 180 - 183: 41.042 distance: 181 - 182: 12.546 distance: 181 - 187: 24.583 distance: 183 - 184: 47.819 distance: 184 - 185: 28.698 distance: 184 - 186: 41.236 distance: 187 - 188: 24.834 distance: 188 - 189: 31.658 distance: 189 - 190: 30.693 distance: 189 - 191: 10.091 distance: 192 - 193: 3.696 distance: 193 - 194: 28.911 distance: 193 - 198: 22.059 distance: 195 - 196: 39.859 distance: 195 - 197: 37.465 distance: 198 - 199: 41.651 distance: 199 - 200: 42.523 distance: 199 - 202: 30.960 distance: 200 - 201: 47.643 distance: 200 - 205: 48.824 distance: 202 - 203: 40.559 distance: 202 - 204: 16.709 distance: 205 - 206: 38.989 distance: 206 - 207: 5.522 distance: 206 - 209: 37.952 distance: 207 - 208: 5.274 distance: 207 - 213: 37.454 distance: 209 - 210: 14.771 distance: 210 - 212: 8.489 distance: 213 - 214: 12.639 distance: 214 - 215: 16.889 distance: 214 - 217: 21.289 distance: 215 - 225: 34.203 distance: 217 - 218: 23.843 distance: 218 - 219: 26.549 distance: 218 - 220: 6.809 distance: 219 - 221: 8.694 distance: 220 - 222: 3.621 distance: 221 - 223: 12.959 distance: 222 - 223: 3.280 distance: 223 - 224: 9.382