Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 07:04:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vum_21390/10_2023/6vum_21390_updated.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 72 5.16 5 C 9868 2.51 5 N 2188 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 14388 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3423 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 17, 'TRANS': 391} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 183 Unusual residues: {'CLR': 3, 'COA': 1, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3VV': 1, 'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'3VV:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 183 Unusual residues: {'CLR': 3, 'COA': 1, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3VV': 1, 'CLR': 2, 'OLA': 1, 'ROV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'3VV:plan-5': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.70, per 1000 atoms: 0.54 Number of scatterers: 14388 At special positions: 0 Unit cell: (109.956, 205.751, 78.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 12 15.00 O 2248 8.00 N 2188 7.00 C 9868 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=0, symmetry=0 Time building additional restraints: 5.88 Conformation dependent library (CDL) restraints added in 2.1 seconds 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.353A pdb=" N GLU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 182 through 206 removed outlier: 3.727A pdb=" N THR A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Proline residue: A 199 - end of helix removed outlier: 4.097A pdb=" N TRP A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 253 through 283 Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 295 through 302 removed outlier: 5.796A pdb=" N PHE A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.631A pdb=" N GLU A 342 " --> pdb=" O TYR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 361 through 384 removed outlier: 4.342A pdb=" N LEU A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix removed outlier: 3.886A pdb=" N LEU A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 447 through 467 removed outlier: 3.993A pdb=" N CYS A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.548A pdb=" N PHE A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 524 removed outlier: 3.525A pdb=" N VAL A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.408A pdb=" N GLU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 181 through 207 Proline residue: B 199 - end of helix removed outlier: 3.941A pdb=" N TRP B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 235 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 250 through 281 removed outlier: 3.737A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.561A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 361 through 384 removed outlier: 4.442A pdb=" N LEU B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix removed outlier: 3.679A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 447 through 468 removed outlier: 3.753A pdb=" N CYS B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 488 removed outlier: 3.741A pdb=" N PHE B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 525 removed outlier: 3.799A pdb=" N THR B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 507 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 509 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 510 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 513 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 515 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 519 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 520 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP B 522 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 523 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 524 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 134 removed outlier: 4.353A pdb=" N GLU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 163 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 182 through 206 removed outlier: 3.727A pdb=" N THR C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 190 " --> pdb=" O TRP C 186 " (cutoff:3.500A) Proline residue: C 199 - end of helix removed outlier: 4.096A pdb=" N TRP C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 No H-bonds generated for 'chain 'C' and resid 209 through 212' Processing helix chain 'C' and resid 219 through 233 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 253 through 283 Proline residue: C 276 - end of helix Processing helix chain 'C' and resid 295 through 302 removed outlier: 5.797A pdb=" N PHE C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 343 removed outlier: 3.631A pdb=" N GLU C 342 " --> pdb=" O TYR C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 384 removed outlier: 4.343A pdb=" N LEU C 371 " --> pdb=" O PHE C 367 " (cutoff:3.500A) Proline residue: C 372 - end of helix removed outlier: 3.887A pdb=" N LEU C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 395 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 447 through 467 removed outlier: 3.993A pdb=" N CYS C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 488 removed outlier: 3.547A pdb=" N PHE C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 485 " --> pdb=" O PHE C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 524 removed outlier: 3.525A pdb=" N VAL C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 removed outlier: 4.408A pdb=" N GLU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 181 through 207 Proline residue: D 199 - end of helix removed outlier: 3.941A pdb=" N TRP D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 207 " --> pdb=" O PHE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 235 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 250 through 281 removed outlier: 3.738A pdb=" N PHE D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Proline residue: D 276 - end of helix Processing helix chain 'D' and resid 294 through 302 removed outlier: 3.560A pdb=" N PHE D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 343 Processing helix chain 'D' and resid 361 through 384 removed outlier: 4.443A pdb=" N LEU D 371 " --> pdb=" O PHE D 367 " (cutoff:3.500A) Proline residue: D 372 - end of helix removed outlier: 3.679A pdb=" N LEU D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 384 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 447 through 468 removed outlier: 3.752A pdb=" N CYS D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 488 removed outlier: 3.741A pdb=" N PHE D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN D 487 " --> pdb=" O GLY D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 525 removed outlier: 3.798A pdb=" N THR D 505 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 507 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 509 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 510 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN D 511 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 513 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 515 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 519 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 520 " --> pdb=" O PHE D 517 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP D 522 " --> pdb=" O SER D 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 523 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 524 " --> pdb=" O GLU D 521 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2010 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: 3.78 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 14837 1.79 - 2.40: 105 2.40 - 3.02: 0 3.02 - 3.63: 0 3.63 - 4.24: 4 Bond restraints: 14946 Sorted by residual: bond pdb=" AO6 COA C 706 " pdb=" AP2 COA C 706 " ideal model delta sigma weight residual 1.610 4.244 -2.634 2.00e-02 2.50e+03 1.73e+04 bond pdb=" AO6 COA A 706 " pdb=" AP2 COA A 706 " ideal model delta sigma weight residual 1.610 4.244 -2.634 2.00e-02 2.50e+03 1.73e+04 bond pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " ideal model delta sigma weight residual 1.610 4.201 -2.591 2.00e-02 2.50e+03 1.68e+04 bond pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " ideal model delta sigma weight residual 1.610 4.201 -2.591 2.00e-02 2.50e+03 1.68e+04 bond pdb=" PC9 COA A 706 " pdb=" PO9 COA A 706 " ideal model delta sigma weight residual 1.410 1.186 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 14941 not shown) Histogram of bond angle deviations from ideal: 15.18 - 39.22: 4 39.22 - 63.25: 0 63.25 - 87.29: 0 87.29 - 111.33: 5281 111.33 - 135.37: 15141 Bond angle restraints: 20426 Sorted by residual: angle pdb=" AO3 COA A 706 " pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " ideal model delta sigma weight residual 102.60 15.18 87.42 3.00e+00 1.11e-01 8.49e+02 angle pdb=" AO3 COA C 706 " pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " ideal model delta sigma weight residual 102.60 15.20 87.40 3.00e+00 1.11e-01 8.49e+02 angle pdb=" AO3 COA A 706 " pdb=" AP2 COA A 706 " pdb=" AO6 COA A 706 " ideal model delta sigma weight residual 102.60 16.44 86.16 3.00e+00 1.11e-01 8.25e+02 angle pdb=" AO3 COA C 706 " pdb=" AP2 COA C 706 " pdb=" AO6 COA C 706 " ideal model delta sigma weight residual 102.60 16.46 86.14 3.00e+00 1.11e-01 8.24e+02 angle pdb=" N63 3VV D 702 " pdb=" C62 3VV D 702 " pdb=" N64 3VV D 702 " ideal model delta sigma weight residual 103.64 121.39 -17.75 3.00e+00 1.11e-01 3.50e+01 ... (remaining 20421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.39: 7893 31.39 - 62.78: 291 62.78 - 94.18: 12 94.18 - 125.57: 2 125.57 - 156.96: 4 Dihedral angle restraints: 8202 sinusoidal: 3310 harmonic: 4892 Sorted by residual: dihedral pdb=" AO3 COA A 706 " pdb=" AP1 COA A 706 " pdb="AO5* COA A 706 " pdb="AC5* COA A 706 " ideal model delta sinusoidal sigma weight residual 291.94 134.98 156.96 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" AO3 COA C 706 " pdb=" AP1 COA C 706 " pdb="AO5* COA C 706 " pdb="AC5* COA C 706 " ideal model delta sinusoidal sigma weight residual 291.94 135.18 156.77 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" AC4 COA A 706 " pdb=" AN9 COA A 706 " pdb="AC1* COA A 706 " pdb="AC2* COA A 706 " ideal model delta sinusoidal sigma weight residual 175.22 -81.04 -103.74 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 8199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1467 0.056 - 0.113: 537 0.113 - 0.169: 113 0.169 - 0.225: 40 0.225 - 0.282: 13 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CA TRP C 320 " pdb=" N TRP C 320 " pdb=" C TRP C 320 " pdb=" CB TRP C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TRP A 320 " pdb=" N TRP A 320 " pdb=" C TRP A 320 " pdb=" CB TRP A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA TRP D 320 " pdb=" N TRP D 320 " pdb=" C TRP D 320 " pdb=" CB TRP D 320 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2167 not shown) Planarity restraints: 2386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 275 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO D 276 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 276 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 276 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 275 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 276 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 275 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 276 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 ... (remaining 2383 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 4 2.31 - 2.96: 5856 2.96 - 3.60: 21123 3.60 - 4.25: 30741 4.25 - 4.90: 54853 Nonbonded interactions: 112577 Sorted by model distance: nonbonded pdb=" AO6 COA A 706 " pdb=" AP1 COA A 706 " model vdw 1.659 2.720 nonbonded pdb=" AO6 COA C 706 " pdb=" AP1 COA C 706 " model vdw 1.659 2.720 nonbonded pdb=" AP2 COA C 706 " pdb="AO5* COA C 706 " model vdw 1.679 2.720 nonbonded pdb=" AP2 COA A 706 " pdb="AO5* COA A 706 " model vdw 1.679 2.720 nonbonded pdb=" N ASN C 409 " pdb=" OD1 ASN C 409 " model vdw 2.381 2.520 ... (remaining 112572 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 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'B' and (resid 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'C' and (resid 118 through 526 or resid 701 or resid 703 through 705)) selection = (chain 'D' and (resid 118 through 526 or resid 701 or resid 703 through 705)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.800 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.710 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.044 2.634 14946 Z= 2.761 Angle : 1.770 87.421 20426 Z= 0.880 Chirality : 0.065 0.282 2170 Planarity : 0.005 0.050 2386 Dihedral : 15.955 156.958 5050 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.12 % Allowed : 3.43 % Favored : 95.45 % 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: -3.29 (0.17), residues: 1628 helix: -1.52 (0.13), residues: 1104 sheet: None (None), residues: 0 loop : -3.46 (0.22), residues: 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 332 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 316 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 327 average time/residue: 0.2450 time to fit residues: 118.8441 Evaluate side-chains 227 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1181 time to fit residues: 2.4519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN A 390 ASN B 204 GLN B 280 ASN B 386 HIS B 500 ASN C 231 GLN C 295 ASN C 296 GLN C 329 GLN C 390 ASN C 500 ASN D 368 ASN D 386 HIS D 500 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14946 Z= 0.234 Angle : 0.744 9.549 20426 Z= 0.358 Chirality : 0.044 0.194 2170 Planarity : 0.005 0.046 2386 Dihedral : 13.691 162.202 2082 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.96 % Allowed : 10.71 % Favored : 87.32 % 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: -1.53 (0.19), residues: 1628 helix: 0.06 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -3.45 (0.22), residues: 516 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 264 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 252 average time/residue: 0.2017 time to fit residues: 81.5530 Evaluate side-chains 232 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1269 time to fit residues: 5.9246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 390 ASN A 500 ASN B 511 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN C 368 ASN C 390 ASN D 204 GLN D 511 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14946 Z= 0.323 Angle : 0.714 6.970 20426 Z= 0.351 Chirality : 0.045 0.156 2170 Planarity : 0.005 0.040 2386 Dihedral : 13.415 165.495 2082 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.40 % Allowed : 14.99 % Favored : 83.61 % 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: -1.19 (0.20), residues: 1628 helix: 0.33 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.45 (0.23), residues: 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 257 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.553 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 248 average time/residue: 0.2153 time to fit residues: 84.2177 Evaluate side-chains 220 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1480 time to fit residues: 5.4504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 295 ASN A 329 GLN B 511 ASN C 231 GLN C 386 HIS C 390 ASN D 511 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14946 Z= 0.177 Angle : 0.630 8.839 20426 Z= 0.308 Chirality : 0.040 0.171 2170 Planarity : 0.004 0.049 2386 Dihedral : 13.053 169.709 2082 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.12 % Allowed : 17.23 % Favored : 81.65 % 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: -0.95 (0.21), residues: 1628 helix: 0.50 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -3.28 (0.24), residues: 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 252 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.484 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 243 average time/residue: 0.2102 time to fit residues: 81.9323 Evaluate side-chains 225 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1399 time to fit residues: 4.3409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 329 GLN B 296 GLN C 231 GLN C 368 ASN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14946 Z= 0.193 Angle : 0.629 10.005 20426 Z= 0.305 Chirality : 0.041 0.169 2170 Planarity : 0.004 0.038 2386 Dihedral : 12.759 172.221 2082 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.61 % Allowed : 17.93 % Favored : 80.46 % 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: -0.78 (0.21), residues: 1628 helix: 0.64 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -3.23 (0.24), residues: 512 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 244 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.504 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 236 average time/residue: 0.2017 time to fit residues: 77.1835 Evaluate side-chains 227 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1364 time to fit residues: 5.6207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14946 Z= 0.217 Angle : 0.637 10.137 20426 Z= 0.310 Chirality : 0.041 0.172 2170 Planarity : 0.004 0.049 2386 Dihedral : 12.623 177.305 2082 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.77 % Allowed : 18.21 % Favored : 81.02 % 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: -0.75 (0.21), residues: 1628 helix: 0.61 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 231 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 1.652 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 225 average time/residue: 0.2209 time to fit residues: 78.7373 Evaluate side-chains 217 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1302 time to fit residues: 3.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN A 329 GLN A 368 ASN B 215 HIS B 223 HIS C 231 GLN D 223 HIS D 296 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.177 Angle : 0.621 8.052 20426 Z= 0.302 Chirality : 0.040 0.176 2170 Planarity : 0.004 0.047 2386 Dihedral : 12.359 179.368 2082 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.85 % Rotamer: Outliers : 0.63 % Allowed : 20.24 % Favored : 79.13 % 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: -0.60 (0.21), residues: 1628 helix: 0.75 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -3.11 (0.25), residues: 508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 231 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 1.534 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 225 average time/residue: 0.2000 time to fit residues: 72.5125 Evaluate side-chains 208 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1414 time to fit residues: 2.9910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 368 ASN B 137 HIS C 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.208 Angle : 0.637 11.705 20426 Z= 0.310 Chirality : 0.040 0.174 2170 Planarity : 0.004 0.047 2386 Dihedral : 12.191 175.890 2082 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.34 % Favored : 90.54 % Rotamer: Outliers : 0.77 % Allowed : 20.73 % Favored : 78.50 % 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: -0.59 (0.21), residues: 1628 helix: 0.76 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -3.08 (0.25), residues: 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 224 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 219 average time/residue: 0.2134 time to fit residues: 75.4240 Evaluate side-chains 208 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1357 time to fit residues: 3.8156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.0270 chunk 44 optimal weight: 0.0270 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 329 GLN C 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14946 Z= 0.162 Angle : 0.627 9.588 20426 Z= 0.304 Chirality : 0.039 0.178 2170 Planarity : 0.004 0.046 2386 Dihedral : 11.844 169.599 2082 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.72 % Favored : 91.15 % Rotamer: Outliers : 0.63 % Allowed : 20.66 % Favored : 78.71 % 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: -0.51 (0.21), residues: 1628 helix: 0.81 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -3.06 (0.25), residues: 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 226 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 221 average time/residue: 0.2118 time to fit residues: 74.2181 Evaluate side-chains 216 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1442 time to fit residues: 3.7030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.0170 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 0.0770 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 386 HIS C 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14946 Z= 0.163 Angle : 0.620 9.862 20426 Z= 0.301 Chirality : 0.039 0.177 2170 Planarity : 0.004 0.048 2386 Dihedral : 11.621 165.519 2082 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.85 % Favored : 91.03 % Rotamer: Outliers : 0.21 % Allowed : 21.08 % Favored : 78.71 % 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: -0.50 (0.21), residues: 1628 helix: 0.82 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -3.01 (0.25), residues: 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3256 Ramachandran restraints generated. 1628 Oldfield, 0 Emsley, 1628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 221 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 218 average time/residue: 0.2055 time to fit residues: 72.0909 Evaluate side-chains 214 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1323 time to fit residues: 2.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.0070 chunk 130 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112196 restraints weight = 20121.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115073 restraints weight = 11509.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116957 restraints weight = 8299.910| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14946 Z= 0.185 Angle : 0.631 9.880 20426 Z= 0.308 Chirality : 0.040 0.177 2170 Planarity : 0.004 0.044 2386 Dihedral : 11.422 159.311 2082 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.03 % Favored : 90.72 % Rotamer: Outliers : 0.28 % Allowed : 21.15 % Favored : 78.57 % 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: -0.39 (0.21), residues: 1628 helix: 0.94 (0.16), residues: 1092 sheet: None (None), residues: 0 loop : -2.90 (0.24), residues: 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.84 seconds wall clock time: 48 minutes 13.10 seconds (2893.10 seconds total)