Starting phenix.real_space_refine on Sun Jul 21 19:19:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsw_32769/07_2024/7wsw_32769.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 88 5.16 5 C 9802 2.51 5 N 2518 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15051 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3735 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3709 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3709 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 16, 'TRANS': 445} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3735 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' K': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 8.22, per 1000 atoms: 0.55 Number of scatterers: 15051 At special positions: 0 Unit cell: (107.167, 115.827, 132.065, 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) K 3 19.00 S 88 16.00 P 4 15.00 O 2636 8.00 N 2518 7.00 C 9802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.32 Conformation dependent library (CDL) restraints added in 2.7 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 67.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.786A pdb=" N TRP A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 82 removed outlier: 4.176A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.501A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 107 removed outlier: 4.204A pdb=" N THR A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 123 through 136 removed outlier: 3.819A pdb=" N ARG A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.577A pdb=" N ALA A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.661A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 215 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.519A pdb=" N ARG A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 293 removed outlier: 3.787A pdb=" N GLY A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.721A pdb=" N ASN A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 347 removed outlier: 3.515A pdb=" N LEU A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.765A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.519A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.881A pdb=" N VAL A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.562A pdb=" N ILE A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.774A pdb=" N MET A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 82 removed outlier: 3.776A pdb=" N VAL B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'B' and resid 86 through 107 removed outlier: 3.760A pdb=" N ILE B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.700A pdb=" N ALA B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.524A pdb=" N LYS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 215 removed outlier: 3.605A pdb=" N ALA B 192 " --> pdb=" O TRP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 235 through 252 Processing helix chain 'B' and resid 263 through 296 removed outlier: 3.573A pdb=" N MET B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 316 removed outlier: 3.745A pdb=" N ARG B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 4.161A pdb=" N GLN B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 4.034A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.575A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 Processing helix chain 'B' and resid 440 through 446 removed outlier: 4.109A pdb=" N VAL B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.636A pdb=" N GLY B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 509 removed outlier: 3.786A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 82 removed outlier: 3.820A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 86 through 107 removed outlier: 3.756A pdb=" N ILE D 91 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR D 92 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.697A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.554A pdb=" N LYS D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 215 removed outlier: 3.597A pdb=" N ALA D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 235 through 252 Processing helix chain 'D' and resid 263 through 296 removed outlier: 3.575A pdb=" N MET D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 316 removed outlier: 3.729A pdb=" N ARG D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 316 " --> pdb=" O PHE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 336 removed outlier: 4.164A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 348 removed outlier: 3.997A pdb=" N GLN D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 364 through 369 removed outlier: 3.609A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 387 Processing helix chain 'D' and resid 440 through 446 removed outlier: 4.111A pdb=" N VAL D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 477 Processing helix chain 'D' and resid 477 through 492 removed outlier: 3.608A pdb=" N GLY D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 509 removed outlier: 3.721A pdb=" N GLU D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 14 Processing helix chain 'C' and resid 54 through 62 removed outlier: 3.785A pdb=" N TRP C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 82 removed outlier: 4.190A pdb=" N VAL C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 107 removed outlier: 4.202A pdb=" N THR C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 123 through 136 removed outlier: 3.817A pdb=" N ARG C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.603A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.660A pdb=" N GLY C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 235 through 252 removed outlier: 3.516A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 293 removed outlier: 3.734A pdb=" N GLY C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.622A pdb=" N ASN C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 347 Processing helix chain 'C' and resid 351 through 368 removed outlier: 3.761A pdb=" N SER C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 386 removed outlier: 3.541A pdb=" N LEU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 removed outlier: 3.883A pdb=" N VAL C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 476 Processing helix chain 'C' and resid 480 through 494 removed outlier: 3.721A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 510 removed outlier: 3.590A pdb=" N MET C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 390 through 393 removed outlier: 6.446A pdb=" N GLN A 461 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 465 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 409 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.575A pdb=" N ASP A 398 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 456 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 400 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 417 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU A 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 419 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A 421 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 428 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 389 through 393 removed outlier: 6.490A pdb=" N GLN B 461 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 409 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 437 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 398 through 400 removed outlier: 6.658A pdb=" N VAL B 454 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG B 431 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP B 421 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE B 429 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 389 through 393 removed outlier: 6.446A pdb=" N GLN D 461 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 398 through 400 removed outlier: 6.665A pdb=" N VAL D 454 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG D 431 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP D 421 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE D 429 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 390 through 393 removed outlier: 6.429A pdb=" N GLN C 461 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 465 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 409 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 397 through 400 removed outlier: 6.578A pdb=" N ASP C 398 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR C 456 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 400 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 417 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU C 432 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 419 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP C 421 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER C 428 " --> pdb=" O ASP C 421 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2520 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: 4.55 Time building geometry restraints manager: 6.88 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: 2507 1.32 - 1.45: 4177 1.45 - 1.57: 8560 1.57 - 1.69: 8 1.69 - 1.82: 148 Bond restraints: 15400 Sorted by residual: bond pdb=" C5 PTY D 901 " pdb=" O14 PTY D 901 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.11e+00 bond pdb=" C5 PTY B 901 " pdb=" O14 PTY B 901 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C5 PTY A 901 " pdb=" O14 PTY A 901 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" C5 PTY C 901 " pdb=" O14 PTY C 901 " ideal model delta sigma weight residual 1.409 1.453 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" O14 PTY B 901 " pdb=" P1 PTY B 901 " ideal model delta sigma weight residual 1.646 1.605 0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 15395 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.77: 375 106.77 - 113.59: 8403 113.59 - 120.40: 5938 120.40 - 127.22: 6032 127.22 - 134.03: 154 Bond angle restraints: 20902 Sorted by residual: angle pdb=" N ASP B 379 " pdb=" CA ASP B 379 " pdb=" C ASP B 379 " ideal model delta sigma weight residual 114.04 109.73 4.31 1.24e+00 6.50e-01 1.21e+01 angle pdb=" O11 PTY B 901 " pdb=" P1 PTY B 901 " pdb=" O14 PTY B 901 " ideal model delta sigma weight residual 92.90 102.99 -10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O11 PTY D 901 " pdb=" P1 PTY D 901 " pdb=" O14 PTY D 901 " ideal model delta sigma weight residual 92.90 102.97 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O11 PTY C 901 " pdb=" P1 PTY C 901 " pdb=" O14 PTY C 901 " ideal model delta sigma weight residual 92.90 102.96 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O11 PTY A 901 " pdb=" P1 PTY A 901 " pdb=" O14 PTY A 901 " ideal model delta sigma weight residual 92.90 102.96 -10.06 3.00e+00 1.11e-01 1.12e+01 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 8187 16.52 - 33.04: 800 33.04 - 49.56: 111 49.56 - 66.09: 29 66.09 - 82.61: 11 Dihedral angle restraints: 9138 sinusoidal: 3614 harmonic: 5524 Sorted by residual: dihedral pdb=" CA MET B 495 " pdb=" C MET B 495 " pdb=" N ASN B 496 " pdb=" CA ASN B 496 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 494 " pdb=" C GLU B 494 " pdb=" N MET B 495 " pdb=" CA MET B 495 " ideal model delta harmonic sigma weight residual -180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN B 126 " pdb=" C GLN B 126 " pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 9135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1873 0.044 - 0.088: 434 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C6 PTY D 901 " pdb=" C1 PTY D 901 " pdb=" C5 PTY D 901 " pdb=" O7 PTY D 901 " both_signs ideal model delta sigma weight residual False 2.49 2.27 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C6 PTY B 901 " pdb=" C1 PTY B 901 " pdb=" C5 PTY B 901 " pdb=" O7 PTY B 901 " both_signs ideal model delta sigma weight residual False 2.49 2.27 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE C 144 " pdb=" N ILE C 144 " pdb=" C ILE C 144 " pdb=" CB ILE C 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2377 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 497 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 498 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO D 88 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 87 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.00e+00 pdb=" N PRO B 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 1670 2.75 - 3.35: 18318 3.35 - 3.94: 28003 3.94 - 4.54: 38060 4.54 - 5.14: 57301 Nonbonded interactions: 143352 Sorted by model distance: nonbonded pdb=" OD2 ASP A 379 " pdb=" OH TYR B 447 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR D 447 " pdb=" OD2 ASP C 379 " model vdw 2.150 2.440 nonbonded pdb=" OG SER A 377 " pdb=" OD1 ASP A 379 " model vdw 2.204 2.440 nonbonded pdb=" O TYR A 273 " pdb=" ND2 ASN A 277 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR A 70 " pdb=" OG1 THR A 92 " model vdw 2.222 2.440 ... (remaining 143347 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 49 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 or (resid 117 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 or (resid 1 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 123 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or r \ esid 338 through 341 or (resid 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 or (resid 344 through 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 395 or (resid 396 and (name N o \ r name CA or name C or name O or name CB )) or resid 397 through 510 or resid 90 \ 1)) selection = (chain 'B' and (resid 49 through 300 or (resid 301 and (name N or name CA or nam \ e C or name O or name CB )) or resid 302 through 313 or (resid 314 through 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 through 320 \ or (resid 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 425 or (resid 426 through 427 and (name N or name C \ A or name C or name O or name CB )) or resid 428 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 503 or \ (resid 504 and (name N or name CA or name C or name O or name CB )) or resid 505 \ or (resid 506 through 510 and (name N or name CA or name C or name O or name CB \ )) or resid 901)) selection = (chain 'C' and (resid 49 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 or (resid 117 through 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 or (resid 1 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 123 through \ 336 or (resid 337 and (name N or name CA or name C or name O or name CB )) or r \ esid 338 through 341 or (resid 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 or (resid 344 through 345 and (name N or name CA or nam \ e C or name O or name CB )) or resid 346 through 395 or (resid 396 and (name N o \ r name CA or name C or name O or name CB )) or resid 397 through 510 or resid 90 \ 1)) selection = (chain 'D' and (resid 49 through 300 or (resid 301 and (name N or name CA or nam \ e C or name O or name CB )) or resid 302 through 313 or (resid 314 through 318 a \ nd (name N or name CA or name C or name O or name CB )) or resid 319 through 320 \ or (resid 321 and (name N or name CA or name C or name O or name CB )) or resid \ 322 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 425 or (resid 426 through 427 and (name N or name C \ A or name C or name O or name CB )) or resid 428 through 499 or (resid 500 and ( \ name N or name CA or name C or name O or name CB )) or resid 501 through 503 or \ (resid 504 and (name N or name CA or name C or name O or name CB )) or resid 505 \ or (resid 506 through 510 and (name N or name CA or name C or name O or name CB \ )) or resid 901)) } 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: 3.650 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: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.620 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.003 0.045 15400 Z= 0.188 Angle : 0.550 10.091 20902 Z= 0.287 Chirality : 0.038 0.220 2380 Planarity : 0.004 0.074 2612 Dihedral : 13.261 82.608 5558 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1856 helix: 1.60 (0.16), residues: 1110 sheet: 0.59 (0.54), residues: 84 loop : -1.59 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 135 HIS 0.008 0.001 HIS C 491 PHE 0.008 0.001 PHE D 409 TYR 0.018 0.001 TYR D 209 ARG 0.009 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.740 Fit side-chains REVERT: A 59 ILE cc_start: 0.9397 (tt) cc_final: 0.9120 (tp) REVERT: A 238 MET cc_start: 0.7626 (tmm) cc_final: 0.7359 (ttt) REVERT: C 59 ILE cc_start: 0.9389 (tt) cc_final: 0.9121 (tp) REVERT: C 238 MET cc_start: 0.7642 (tmm) cc_final: 0.7372 (ttt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2405 time to fit residues: 46.4005 Evaluate side-chains 104 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.0000 chunk 88 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15400 Z= 0.226 Angle : 0.518 7.141 20902 Z= 0.270 Chirality : 0.039 0.142 2380 Planarity : 0.004 0.063 2612 Dihedral : 5.618 57.582 2188 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.57 % Allowed : 4.89 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1856 helix: 1.64 (0.16), residues: 1138 sheet: 0.76 (0.54), residues: 66 loop : -1.64 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 135 HIS 0.004 0.001 HIS A 491 PHE 0.016 0.001 PHE D 160 TYR 0.014 0.001 TYR C 209 ARG 0.011 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.853 Fit side-chains REVERT: A 59 ILE cc_start: 0.9442 (tt) cc_final: 0.9206 (tp) REVERT: C 59 ILE cc_start: 0.9439 (tt) cc_final: 0.9202 (tp) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.2486 time to fit residues: 44.2501 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 0.0870 chunk 135 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15400 Z= 0.133 Angle : 0.474 7.507 20902 Z= 0.244 Chirality : 0.037 0.133 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.255 59.825 2188 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.51 % Allowed : 7.30 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1856 helix: 1.87 (0.16), residues: 1144 sheet: 0.51 (0.53), residues: 66 loop : -1.79 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 135 HIS 0.002 0.000 HIS D 491 PHE 0.010 0.001 PHE D 409 TYR 0.012 0.001 TYR D 210 ARG 0.007 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.722 Fit side-chains REVERT: A 59 ILE cc_start: 0.9454 (tt) cc_final: 0.9204 (tp) REVERT: A 238 MET cc_start: 0.7555 (tmm) cc_final: 0.7328 (tmm) REVERT: B 352 LYS cc_start: 0.8997 (tptp) cc_final: 0.8782 (tptp) REVERT: D 376 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7765 (p) REVERT: C 59 ILE cc_start: 0.9451 (tt) cc_final: 0.9201 (tp) REVERT: C 238 MET cc_start: 0.7568 (tmm) cc_final: 0.7339 (tmm) outliers start: 8 outliers final: 2 residues processed: 114 average time/residue: 0.2251 time to fit residues: 41.3370 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 0.0570 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 0.0980 chunk 179 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15400 Z= 0.208 Angle : 0.490 7.716 20902 Z= 0.255 Chirality : 0.038 0.138 2380 Planarity : 0.004 0.064 2612 Dihedral : 5.378 57.584 2188 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.70 % Allowed : 9.58 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1856 helix: 1.87 (0.16), residues: 1162 sheet: 0.50 (0.54), residues: 66 loop : -1.82 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 135 HIS 0.002 0.001 HIS C 329 PHE 0.010 0.001 PHE D 409 TYR 0.012 0.001 TYR D 210 ARG 0.007 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.804 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 111 average time/residue: 0.2464 time to fit residues: 43.5993 Evaluate side-chains 105 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15400 Z= 0.146 Angle : 0.470 6.814 20902 Z= 0.243 Chirality : 0.037 0.134 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.211 53.223 2188 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.44 % Allowed : 11.10 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1856 helix: 1.94 (0.16), residues: 1156 sheet: 0.40 (0.54), residues: 66 loop : -1.77 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 135 HIS 0.003 0.001 HIS A 491 PHE 0.015 0.001 PHE D 160 TYR 0.013 0.001 TYR D 210 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7576 (tmm) cc_final: 0.7366 (tmm) REVERT: D 376 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7659 (p) REVERT: C 238 MET cc_start: 0.7589 (tmm) cc_final: 0.7378 (tmm) outliers start: 7 outliers final: 3 residues processed: 109 average time/residue: 0.2575 time to fit residues: 45.5217 Evaluate side-chains 106 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15400 Z= 0.267 Angle : 0.518 6.647 20902 Z= 0.270 Chirality : 0.039 0.141 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.656 56.044 2188 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.76 % Allowed : 11.80 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1856 helix: 1.80 (0.16), residues: 1164 sheet: -0.14 (0.51), residues: 86 loop : -1.68 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 135 HIS 0.003 0.001 HIS A 294 PHE 0.011 0.001 PHE D 409 TYR 0.012 0.001 TYR B 210 ARG 0.003 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.2308 time to fit residues: 40.0482 Evaluate side-chains 107 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15400 Z= 0.144 Angle : 0.473 7.338 20902 Z= 0.244 Chirality : 0.038 0.133 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.353 53.107 2188 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.57 % Allowed : 12.69 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1856 helix: 1.90 (0.16), residues: 1168 sheet: 0.37 (0.55), residues: 66 loop : -1.65 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 135 HIS 0.002 0.001 HIS B 360 PHE 0.011 0.001 PHE D 409 TYR 0.013 0.001 TYR D 210 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8530 (ttp) cc_final: 0.7804 (tmm) outliers start: 9 outliers final: 9 residues processed: 110 average time/residue: 0.2406 time to fit residues: 42.6867 Evaluate side-chains 111 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.0000 overall best weight: 0.7826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15400 Z= 0.145 Angle : 0.476 9.050 20902 Z= 0.245 Chirality : 0.037 0.132 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.147 45.001 2188 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.76 % Allowed : 13.01 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.21), residues: 1856 helix: 1.95 (0.16), residues: 1174 sheet: 0.31 (0.55), residues: 66 loop : -1.69 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 135 HIS 0.002 0.001 HIS C 329 PHE 0.012 0.001 PHE D 409 TYR 0.013 0.001 TYR B 210 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8511 (ttp) cc_final: 0.7788 (tmm) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 0.2415 time to fit residues: 43.8544 Evaluate side-chains 111 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15400 Z= 0.243 Angle : 0.508 8.382 20902 Z= 0.264 Chirality : 0.039 0.138 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.401 49.058 2188 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.82 % Allowed : 12.94 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1856 helix: 1.86 (0.16), residues: 1168 sheet: -0.14 (0.51), residues: 86 loop : -1.62 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 135 HIS 0.002 0.001 HIS B 360 PHE 0.011 0.001 PHE D 409 TYR 0.013 0.001 TYR D 210 ARG 0.007 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8559 (ttp) cc_final: 0.7788 (tmm) outliers start: 13 outliers final: 12 residues processed: 112 average time/residue: 0.2266 time to fit residues: 41.0190 Evaluate side-chains 115 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15400 Z= 0.206 Angle : 0.496 8.449 20902 Z= 0.257 Chirality : 0.038 0.135 2380 Planarity : 0.004 0.066 2612 Dihedral : 5.400 51.299 2188 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.76 % Allowed : 13.13 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1856 helix: 1.87 (0.16), residues: 1168 sheet: -0.16 (0.51), residues: 86 loop : -1.62 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 135 HIS 0.002 0.001 HIS B 360 PHE 0.011 0.001 PHE D 409 TYR 0.013 0.001 TYR D 210 ARG 0.007 0.000 ARG B 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8575 (ttp) cc_final: 0.7815 (tmm) outliers start: 12 outliers final: 12 residues processed: 109 average time/residue: 0.2310 time to fit residues: 40.7531 Evaluate side-chains 115 residues out of total 1670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 45 optimal weight: 0.0030 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070786 restraints weight = 38750.768| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.43 r_work: 0.2964 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15400 Z= 0.142 Angle : 0.471 8.619 20902 Z= 0.244 Chirality : 0.037 0.132 2380 Planarity : 0.004 0.065 2612 Dihedral : 5.173 48.106 2188 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.70 % Allowed : 13.13 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1856 helix: 1.95 (0.16), residues: 1174 sheet: -0.20 (0.51), residues: 86 loop : -1.61 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 135 HIS 0.002 0.001 HIS B 360 PHE 0.011 0.001 PHE D 409 TYR 0.013 0.001 TYR B 210 ARG 0.007 0.000 ARG B 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.12 seconds wall clock time: 49 minutes 29.06 seconds (2969.06 seconds total)