Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:22:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/04_2023/7u2m_26315_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.333 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 9200 2.51 5 N 2285 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14155 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.18, per 1000 atoms: 0.58 Number of scatterers: 14155 At special positions: 0 Unit cell: (105.537, 106.368, 135.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2565 8.00 N 2285 7.00 C 9200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 36.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.517A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.560A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 326 removed outlier: 3.576A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 424 removed outlier: 4.330A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.800A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 106 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.517A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.560A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 326 removed outlier: 3.576A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 424 removed outlier: 4.331A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.800A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.517A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.559A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 326 removed outlier: 3.575A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 424 removed outlier: 4.331A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.800A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.517A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.560A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 326 removed outlier: 3.575A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 424 removed outlier: 4.330A pdb=" N LYS D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.800A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 244 through 255 removed outlier: 3.517A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.560A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 326 removed outlier: 3.576A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 424 removed outlier: 4.330A pdb=" N LYS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.801A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 5.789A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 167 through 173 Processing sheet with id= D, first strand: chain 'A' and resid 203 through 205 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 5.790A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= G, first strand: chain 'B' and resid 167 through 173 Processing sheet with id= H, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 5.790A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= K, first strand: chain 'C' and resid 167 through 173 Processing sheet with id= L, first strand: chain 'C' and resid 203 through 205 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 5.789A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= O, first strand: chain 'D' and resid 167 through 173 Processing sheet with id= P, first strand: chain 'D' and resid 203 through 205 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 5.788A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= S, first strand: chain 'E' and resid 167 through 173 Processing sheet with id= T, first strand: chain 'E' and resid 203 through 205 560 hydrogen bonds defined for protein. 1650 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: 4.18 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4355 1.34 - 1.46: 3586 1.46 - 1.58: 6384 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 14500 Sorted by residual: bond pdb=" C LEU D 200 " pdb=" N PRO D 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.81e+00 bond pdb=" C LEU B 200 " pdb=" N PRO B 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.72e+00 bond pdb=" C LEU A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.65e+00 bond pdb=" C LEU E 200 " pdb=" N PRO E 201 " ideal model delta sigma weight residual 1.336 1.317 0.019 1.20e-02 6.94e+03 2.61e+00 bond pdb=" C LEU C 200 " pdb=" N PRO C 201 " ideal model delta sigma weight residual 1.336 1.317 0.019 1.20e-02 6.94e+03 2.51e+00 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.54: 363 105.54 - 112.65: 7668 112.65 - 119.76: 4664 119.76 - 126.87: 6780 126.87 - 133.98: 205 Bond angle restraints: 19680 Sorted by residual: angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N THR E 128 " pdb=" CA THR E 128 " pdb=" CB THR E 128 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N THR D 128 " pdb=" CA THR D 128 " pdb=" CB THR D 128 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N THR C 128 " pdb=" CA THR C 128 " pdb=" CB THR C 128 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N THR A 128 " pdb=" CA THR A 128 " pdb=" CB THR A 128 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.37e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 8192 15.32 - 30.63: 313 30.63 - 45.95: 35 45.95 - 61.27: 10 61.27 - 76.58: 5 Dihedral angle restraints: 8555 sinusoidal: 3440 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.38 47.62 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.42 47.58 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 8552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1676 0.052 - 0.103: 483 0.103 - 0.155: 81 0.155 - 0.206: 10 0.206 - 0.258: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2252 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C VAL C 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL C 151 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 151 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C VAL E 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL E 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 151 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C VAL D 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL D 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 152 " 0.012 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 13828 3.20 - 3.76: 20771 3.76 - 4.33: 31992 4.33 - 4.90: 49761 Nonbonded interactions: 116522 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" OG SER E 27 " model vdw 2.059 2.440 nonbonded pdb=" OG SER D 27 " pdb=" OD2 ASP E 41 " model vdw 2.060 2.440 nonbonded pdb=" OG SER C 27 " pdb=" OD2 ASP D 41 " model vdw 2.064 2.440 nonbonded pdb=" OG SER A 27 " pdb=" OD2 ASP B 41 " model vdw 2.073 2.440 nonbonded pdb=" OG SER B 27 " pdb=" OD2 ASP C 41 " model vdw 2.077 2.440 ... (remaining 116517 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 8.190 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.900 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.008 0.045 14500 Z= 0.513 Angle : 0.851 6.608 19680 Z= 0.474 Chirality : 0.050 0.258 2255 Planarity : 0.004 0.032 2435 Dihedral : 8.961 76.584 5205 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.00 % 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: -3.83 (0.18), residues: 1710 helix: -2.67 (0.17), residues: 525 sheet: -2.27 (0.23), residues: 395 loop : -2.48 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.0982 time to fit residues: 747.4964 Evaluate side-chains 437 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 141 ASN A 166 GLN A 171 GLN A 202 GLN A 219 ASN A 231 HIS B 62 ASN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 141 ASN B 171 GLN B 202 GLN B 219 ASN B 231 HIS B 242 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 141 ASN C 166 GLN C 202 GLN C 231 HIS C 242 GLN C 321 ASN D 62 ASN D 77 ASN D 83 GLN D 141 ASN D 202 GLN D 219 ASN D 231 HIS D 242 GLN D 321 ASN E 62 ASN E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 141 ASN E 171 GLN E 202 GLN E 219 ASN E 231 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 14500 Z= 0.229 Angle : 0.746 10.977 19680 Z= 0.375 Chirality : 0.049 0.184 2255 Planarity : 0.005 0.041 2435 Dihedral : 5.674 37.217 1885 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 4.72 % 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: -2.42 (0.19), residues: 1710 helix: -1.00 (0.20), residues: 615 sheet: -1.28 (0.25), residues: 345 loop : -2.22 (0.22), residues: 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 466 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 28 residues processed: 484 average time/residue: 1.0519 time to fit residues: 565.5369 Evaluate side-chains 419 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 391 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 4 residues processed: 25 average time/residue: 0.4584 time to fit residues: 16.7181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 202 GLN A 242 GLN B 47 ASN B 83 GLN B 171 GLN B 202 GLN B 321 ASN C 47 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 47 ASN D 82 GLN D 83 GLN D 166 GLN D 202 GLN D 326 GLN E 47 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 171 GLN E 202 GLN E 321 ASN E 326 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 14500 Z= 0.322 Angle : 0.710 7.644 19680 Z= 0.362 Chirality : 0.048 0.154 2255 Planarity : 0.005 0.049 2435 Dihedral : 5.308 28.254 1885 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 7.34 % 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: -1.56 (0.20), residues: 1710 helix: -0.02 (0.21), residues: 610 sheet: -0.77 (0.25), residues: 345 loop : -1.99 (0.22), residues: 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 417 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 44 residues processed: 448 average time/residue: 1.1217 time to fit residues: 555.4715 Evaluate side-chains 423 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 379 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 9 residues processed: 36 average time/residue: 0.4930 time to fit residues: 24.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 81 optimal weight: 0.0770 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 82 GLN A 202 GLN B 47 ASN B 82 GLN B 83 GLN B 202 GLN C 47 ASN C 82 GLN C 202 GLN D 47 ASN D 202 GLN D 219 ASN D 326 GLN E 47 ASN E 202 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14500 Z= 0.182 Angle : 0.664 9.124 19680 Z= 0.329 Chirality : 0.046 0.166 2255 Planarity : 0.004 0.047 2435 Dihedral : 4.901 19.157 1885 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 5.57 % 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: -1.09 (0.20), residues: 1710 helix: 0.38 (0.21), residues: 615 sheet: -0.53 (0.26), residues: 345 loop : -1.75 (0.22), residues: 750 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 428 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 42 residues processed: 453 average time/residue: 1.1033 time to fit residues: 555.2138 Evaluate side-chains 422 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 380 time to evaluate : 1.574 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 11 residues processed: 31 average time/residue: 0.4645 time to fit residues: 20.0861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 131 ASN A 202 GLN A 321 ASN B 47 ASN B 83 GLN B 131 ASN B 202 GLN C 47 ASN C 83 GLN C 202 GLN C 235 GLN D 47 ASN E 47 ASN E 82 GLN E 131 ASN E 202 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 14500 Z= 0.316 Angle : 0.686 7.877 19680 Z= 0.344 Chirality : 0.047 0.145 2255 Planarity : 0.004 0.049 2435 Dihedral : 4.869 20.022 1885 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 6.03 % 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 (0.20), residues: 1710 helix: 0.54 (0.21), residues: 625 sheet: -0.47 (0.26), residues: 345 loop : -1.69 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 387 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 55 residues processed: 406 average time/residue: 1.0984 time to fit residues: 494.3398 Evaluate side-chains 419 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 364 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 15 residues processed: 40 average time/residue: 0.6875 time to fit residues: 35.0504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN C 47 ASN C 202 GLN D 47 ASN D 62 ASN D 202 GLN D 326 GLN E 47 ASN E 321 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 14500 Z= 0.280 Angle : 0.675 8.276 19680 Z= 0.339 Chirality : 0.047 0.179 2255 Planarity : 0.004 0.049 2435 Dihedral : 4.787 20.053 1885 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 5.84 % 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: -0.73 (0.20), residues: 1710 helix: 0.80 (0.22), residues: 625 sheet: -0.48 (0.25), residues: 345 loop : -1.61 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 388 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 60 residues processed: 414 average time/residue: 1.0990 time to fit residues: 504.7777 Evaluate side-chains 425 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 365 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 19 residues processed: 41 average time/residue: 0.5722 time to fit residues: 30.2680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 91 optimal weight: 0.0670 chunk 163 optimal weight: 0.4980 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN C 47 ASN C 202 GLN D 47 ASN D 202 GLN D 219 ASN E 47 ASN E 321 ASN E 326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14500 Z= 0.182 Angle : 0.635 8.242 19680 Z= 0.316 Chirality : 0.045 0.193 2255 Planarity : 0.004 0.048 2435 Dihedral : 4.566 19.365 1885 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 5.57 % 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: -0.56 (0.20), residues: 1710 helix: 1.02 (0.22), residues: 625 sheet: -0.45 (0.25), residues: 345 loop : -1.56 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 385 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 48 residues processed: 421 average time/residue: 1.0749 time to fit residues: 504.7563 Evaluate side-chains 411 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 22 residues processed: 27 average time/residue: 0.5043 time to fit residues: 18.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 326 GLN B 47 ASN C 47 ASN C 202 GLN D 47 ASN D 62 ASN D 202 GLN E 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 14500 Z= 0.241 Angle : 0.671 8.533 19680 Z= 0.334 Chirality : 0.046 0.188 2255 Planarity : 0.004 0.048 2435 Dihedral : 4.590 19.514 1885 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 5.05 % 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: -0.43 (0.20), residues: 1710 helix: 1.18 (0.22), residues: 625 sheet: -0.38 (0.25), residues: 345 loop : -1.52 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 379 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 60 residues processed: 406 average time/residue: 1.0828 time to fit residues: 489.2250 Evaluate side-chains 422 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 362 time to evaluate : 1.751 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 24 residues processed: 37 average time/residue: 0.5542 time to fit residues: 26.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.0770 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 0.0000 chunk 100 optimal weight: 0.3980 chunk 161 optimal weight: 0.9980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 171 GLN A 326 GLN B 47 ASN C 47 ASN C 202 GLN D 47 ASN D 202 GLN E 47 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14500 Z= 0.178 Angle : 0.654 8.744 19680 Z= 0.321 Chirality : 0.045 0.174 2255 Planarity : 0.004 0.048 2435 Dihedral : 4.468 21.034 1885 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.87 % 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: -0.35 (0.20), residues: 1710 helix: 1.28 (0.22), residues: 625 sheet: -0.28 (0.26), residues: 345 loop : -1.54 (0.21), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 390 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 45 residues processed: 417 average time/residue: 1.0564 time to fit residues: 490.0215 Evaluate side-chains 409 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 364 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 24 residues processed: 22 average time/residue: 0.5386 time to fit residues: 16.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN C 47 ASN C 202 GLN D 47 ASN D 202 GLN D 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14500 Z= 0.227 Angle : 0.696 9.437 19680 Z= 0.343 Chirality : 0.046 0.188 2255 Planarity : 0.004 0.048 2435 Dihedral : 4.561 23.305 1885 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 3.28 % 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: -0.37 (0.20), residues: 1710 helix: 1.21 (0.22), residues: 625 sheet: -0.14 (0.26), residues: 340 loop : -1.58 (0.21), residues: 745 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 377 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 40 residues processed: 403 average time/residue: 1.0704 time to fit residues: 483.3475 Evaluate side-chains 400 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 360 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 23 residues processed: 18 average time/residue: 0.5052 time to fit residues: 13.8269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0000 chunk 118 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 overall best weight: 0.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 326 GLN B 47 ASN C 202 GLN D 47 ASN D 202 GLN E 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112730 restraints weight = 21587.252| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.77 r_work: 0.3123 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14500 Z= 0.176 Angle : 0.675 9.581 19680 Z= 0.332 Chirality : 0.046 0.172 2255 Planarity : 0.004 0.048 2435 Dihedral : 4.439 29.067 1885 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 2.75 % 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: -0.36 (0.20), residues: 1710 helix: 1.20 (0.22), residues: 625 sheet: -0.05 (0.26), residues: 340 loop : -1.62 (0.21), residues: 745 =============================================================================== Job complete usr+sys time: 7536.99 seconds wall clock time: 133 minutes 22.44 seconds (8002.44 seconds total)