Starting phenix.real_space_refine on Sat Mar 16 08:39:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2m_26315/03_2024/7u2m_26315_trim_updated.pdb" } resolution = 2.9 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= 0.002 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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: 7.40, per 1000 atoms: 0.52 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: 5.93 Conformation dependent library (CDL) restraints added in 2.6 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: 3.13 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: 4.00 Time building geometry restraints manager: 6.39 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 - 22.24: 8600 22.24 - 44.48: 175 44.48 - 66.73: 40 66.73 - 88.97: 35 88.97 - 111.21: 20 Dihedral angle restraints: 8870 sinusoidal: 3755 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 8867 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.560 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.260 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.010 ------------------------------------------------------------------------------- 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= 0.514 Angle : 0.878 11.068 19680 Z= 0.479 Chirality : 0.050 0.258 2255 Planarity : 0.004 0.032 2435 Dihedral : 13.141 111.210 5520 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 % Allowed : 2.62 % Favored : 97.38 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 302 HIS 0.005 0.003 HIS C 231 PHE 0.015 0.003 PHE D 258 TYR 0.023 0.002 TYR B 144 ARG 0.006 0.001 ARG D 212 *********************** 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 : 1.787 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 REVERT: A 127 VAL cc_start: 0.8427 (t) cc_final: 0.8219 (p) REVERT: A 137 SER cc_start: 0.8754 (m) cc_final: 0.8343 (p) REVERT: A 139 ASN cc_start: 0.8500 (p0) cc_final: 0.8134 (p0) REVERT: A 166 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8449 (mm110) REVERT: A 202 GLN cc_start: 0.8606 (mt0) cc_final: 0.8376 (tt0) REVERT: A 286 SER cc_start: 0.9364 (p) cc_final: 0.9117 (p) REVERT: A 317 TYR cc_start: 0.8602 (t80) cc_final: 0.8292 (t80) REVERT: A 395 PHE cc_start: 0.8708 (m-10) cc_final: 0.8474 (m-10) REVERT: B 202 GLN cc_start: 0.8499 (mt0) cc_final: 0.8096 (mt0) REVERT: B 424 THR cc_start: 0.9031 (m) cc_final: 0.8812 (m) REVERT: C 33 LEU cc_start: 0.8736 (tp) cc_final: 0.8487 (tp) REVERT: C 127 VAL cc_start: 0.8460 (t) cc_final: 0.8202 (p) REVERT: C 202 GLN cc_start: 0.8527 (mt0) cc_final: 0.8140 (mt0) REVERT: C 395 PHE cc_start: 0.8678 (m-10) cc_final: 0.8460 (m-10) REVERT: D 43 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.8749 (mtm-85) REVERT: D 63 SER cc_start: 0.8466 (t) cc_final: 0.8085 (p) REVERT: D 189 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8540 (tppt) REVERT: D 202 GLN cc_start: 0.8554 (mt0) cc_final: 0.8186 (mt0) REVERT: D 400 LYS cc_start: 0.9221 (ttmm) cc_final: 0.9013 (mmmm) REVERT: E 47 ASN cc_start: 0.9249 (m-40) cc_final: 0.9004 (m-40) REVERT: E 63 SER cc_start: 0.8435 (t) cc_final: 0.8092 (p) REVERT: E 139 ASN cc_start: 0.8580 (p0) cc_final: 0.8265 (p0) REVERT: E 189 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8479 (tppt) REVERT: E 202 GLN cc_start: 0.8562 (mt0) cc_final: 0.8263 (mt0) REVERT: E 222 LYS cc_start: 0.8053 (ptmm) cc_final: 0.7648 (pttt) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.0483 time to fit residues: 715.0782 Evaluate side-chains 442 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 171 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 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 231 HIS C 242 GLN C 321 ASN D 62 ASN D 77 ASN D 83 GLN D 141 ASN 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 219 ASN E 231 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14500 Z= 0.234 Angle : 0.751 10.560 19680 Z= 0.375 Chirality : 0.049 0.160 2255 Planarity : 0.005 0.042 2435 Dihedral : 11.543 67.546 2200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.13 % Allowed : 18.75 % Favored : 77.11 % 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: -2.45 (0.19), residues: 1710 helix: -1.02 (0.20), residues: 615 sheet: -1.27 (0.24), residues: 345 loop : -2.24 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.002 0.001 HIS E 231 PHE 0.025 0.002 PHE D 311 TYR 0.036 0.002 TYR C 317 ARG 0.006 0.001 ARG D 212 *********************** 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 526 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 463 time to evaluate : 1.709 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: A 133 LEU cc_start: 0.8380 (tp) cc_final: 0.8163 (tt) REVERT: A 139 ASN cc_start: 0.8616 (p0) cc_final: 0.8369 (p0) REVERT: A 202 GLN cc_start: 0.8526 (mt0) cc_final: 0.8314 (mt0) REVERT: A 204 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8211 (mt) REVERT: A 249 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 271 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8922 (tp) REVERT: A 274 THR cc_start: 0.9240 (m) cc_final: 0.8999 (p) REVERT: B 133 LEU cc_start: 0.8392 (tp) cc_final: 0.8075 (tt) REVERT: B 202 GLN cc_start: 0.8541 (mt0) cc_final: 0.8146 (mt0) REVERT: B 204 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 249 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 133 LEU cc_start: 0.8419 (tp) cc_final: 0.8190 (tt) REVERT: C 249 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8084 (mp) REVERT: C 289 SER cc_start: 0.9082 (t) cc_final: 0.8777 (p) REVERT: C 316 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 63 SER cc_start: 0.8645 (t) cc_final: 0.8415 (p) REVERT: D 133 LEU cc_start: 0.8465 (tp) cc_final: 0.8238 (tt) REVERT: D 204 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8203 (mt) REVERT: D 229 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7909 (mtt-85) REVERT: D 274 THR cc_start: 0.9077 (m) cc_final: 0.8820 (p) REVERT: D 289 SER cc_start: 0.9027 (t) cc_final: 0.8800 (p) REVERT: D 316 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 398 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7823 (mmt90) REVERT: E 47 ASN cc_start: 0.9169 (m-40) cc_final: 0.8959 (m110) REVERT: E 63 SER cc_start: 0.8583 (t) cc_final: 0.8358 (p) REVERT: E 133 LEU cc_start: 0.8483 (tp) cc_final: 0.8240 (tt) REVERT: E 139 ASN cc_start: 0.8663 (p0) cc_final: 0.8358 (p0) REVERT: E 179 MET cc_start: 0.8737 (mmm) cc_final: 0.8372 (mmm) REVERT: E 202 GLN cc_start: 0.8559 (mt0) cc_final: 0.8253 (mt0) REVERT: E 204 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8304 (mt) REVERT: E 212 ARG cc_start: 0.8074 (ptp-170) cc_final: 0.7789 (ptp-170) REVERT: E 249 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8203 (mp) REVERT: E 316 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7592 (tm-30) outliers start: 63 outliers final: 28 residues processed: 478 average time/residue: 1.0683 time to fit residues: 566.7377 Evaluate side-chains 443 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 406 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 242 GLN A 321 ASN B 47 ASN B 171 GLN B 321 ASN C 47 ASN C 82 GLN D 47 ASN D 82 GLN D 166 GLN D 326 GLN E 83 GLN E 171 GLN E 321 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14500 Z= 0.234 Angle : 0.690 7.903 19680 Z= 0.342 Chirality : 0.047 0.157 2255 Planarity : 0.004 0.047 2435 Dihedral : 8.323 50.101 2200 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.10 % Allowed : 20.66 % Favored : 73.25 % 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: -1.47 (0.20), residues: 1710 helix: 0.07 (0.21), residues: 610 sheet: -0.70 (0.26), residues: 345 loop : -1.98 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 186 HIS 0.003 0.001 HIS E 125 PHE 0.022 0.002 PHE E 311 TYR 0.031 0.002 TYR C 317 ARG 0.006 0.000 ARG A 229 *********************** 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 522 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 429 time to evaluate : 1.721 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: A 139 ASN cc_start: 0.8650 (p0) cc_final: 0.8397 (p0) REVERT: A 156 MET cc_start: 0.9061 (mmm) cc_final: 0.8762 (mmm) REVERT: A 204 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 133 LEU cc_start: 0.8469 (tp) cc_final: 0.8147 (tt) REVERT: B 202 GLN cc_start: 0.8548 (mt0) cc_final: 0.8136 (mt0) REVERT: B 204 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (mt) REVERT: C 133 LEU cc_start: 0.8506 (tp) cc_final: 0.8293 (tt) REVERT: C 173 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 202 GLN cc_start: 0.8419 (mt0) cc_final: 0.8218 (mt0) REVERT: D 63 SER cc_start: 0.8728 (t) cc_final: 0.8487 (p) REVERT: D 100 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: D 202 GLN cc_start: 0.8380 (mt0) cc_final: 0.8046 (mt0) REVERT: D 204 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8200 (mt) REVERT: D 212 ARG cc_start: 0.7983 (ptp-170) cc_final: 0.7078 (ptt180) REVERT: D 229 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7302 (mtt-85) REVERT: E 32 LYS cc_start: 0.8815 (mttt) cc_final: 0.8607 (ttmt) REVERT: E 63 SER cc_start: 0.8608 (t) cc_final: 0.8376 (p) REVERT: E 133 LEU cc_start: 0.8522 (tp) cc_final: 0.8257 (tt) REVERT: E 139 ASN cc_start: 0.8674 (p0) cc_final: 0.8282 (p0) REVERT: E 156 MET cc_start: 0.9024 (mmm) cc_final: 0.8743 (mmm) REVERT: E 159 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: E 179 MET cc_start: 0.8694 (mmm) cc_final: 0.8343 (mmm) REVERT: E 202 GLN cc_start: 0.8554 (mt0) cc_final: 0.8250 (mt0) REVERT: E 249 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8154 (mp) REVERT: E 316 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7653 (tm-30) outliers start: 93 outliers final: 38 residues processed: 460 average time/residue: 1.0346 time to fit residues: 528.4383 Evaluate side-chains 438 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 393 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 326 GLN B 47 ASN B 82 GLN B 83 GLN C 47 ASN C 83 GLN D 47 ASN D 83 GLN D 219 ASN E 47 ASN E 321 ASN E 326 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14500 Z= 0.276 Angle : 0.689 8.812 19680 Z= 0.341 Chirality : 0.047 0.163 2255 Planarity : 0.004 0.049 2435 Dihedral : 6.709 47.092 2200 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.36 % Allowed : 21.57 % Favored : 72.07 % 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: 0.47 (0.21), residues: 615 sheet: -0.55 (0.26), residues: 345 loop : -1.82 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 422 HIS 0.002 0.001 HIS E 125 PHE 0.019 0.002 PHE E 311 TYR 0.030 0.002 TYR E 317 ARG 0.005 0.000 ARG A 229 *********************** 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 507 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 410 time to evaluate : 1.812 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: A 105 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6736 (mpm) REVERT: A 139 ASN cc_start: 0.8601 (p0) cc_final: 0.8373 (p0) REVERT: A 204 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 242 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 249 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 32 LYS cc_start: 0.8777 (mttt) cc_final: 0.8559 (ttmt) REVERT: B 133 LEU cc_start: 0.8476 (tp) cc_final: 0.8167 (tt) REVERT: B 171 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: B 202 GLN cc_start: 0.8505 (mt0) cc_final: 0.8102 (mt0) REVERT: B 249 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8096 (mp) REVERT: C 105 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6967 (mpm) REVERT: C 173 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: D 63 SER cc_start: 0.8745 (t) cc_final: 0.8484 (p) REVERT: D 100 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: D 179 MET cc_start: 0.8675 (mmm) cc_final: 0.8291 (mmm) REVERT: D 202 GLN cc_start: 0.8385 (mt0) cc_final: 0.8060 (mt0) REVERT: D 204 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8270 (mt) REVERT: D 249 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8163 (mp) REVERT: E 49 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8185 (mmtt) REVERT: E 63 SER cc_start: 0.8674 (t) cc_final: 0.8417 (p) REVERT: E 133 LEU cc_start: 0.8520 (tp) cc_final: 0.8275 (tt) REVERT: E 139 ASN cc_start: 0.8616 (p0) cc_final: 0.8252 (p0) REVERT: E 159 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8001 (tmtt) REVERT: E 179 MET cc_start: 0.8678 (mmm) cc_final: 0.8251 (mmm) REVERT: E 202 GLN cc_start: 0.8527 (mt0) cc_final: 0.8251 (tt0) REVERT: E 249 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8135 (mp) outliers start: 97 outliers final: 55 residues processed: 442 average time/residue: 1.0712 time to fit residues: 525.3197 Evaluate side-chains 442 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 374 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 D 47 ASN D 326 GLN E 47 ASN E 82 GLN E 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14500 Z= 0.252 Angle : 0.668 8.547 19680 Z= 0.331 Chirality : 0.046 0.174 2255 Planarity : 0.004 0.049 2435 Dihedral : 6.099 41.820 2200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.69 % Allowed : 22.03 % Favored : 71.28 % 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: -0.92 (0.20), residues: 1710 helix: 0.62 (0.22), residues: 625 sheet: -0.47 (0.25), residues: 345 loop : -1.75 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 422 HIS 0.002 0.001 HIS E 125 PHE 0.018 0.002 PHE E 311 TYR 0.029 0.002 TYR E 317 ARG 0.004 0.000 ARG A 229 *********************** 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 501 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 399 time to evaluate : 1.681 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: A 139 ASN cc_start: 0.8614 (p0) cc_final: 0.8409 (p0) REVERT: A 204 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 242 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 249 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 395 PHE cc_start: 0.8750 (m-10) cc_final: 0.8549 (m-10) REVERT: B 97 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7723 (t0) REVERT: B 105 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6689 (mpm) REVERT: B 133 LEU cc_start: 0.8526 (tp) cc_final: 0.8244 (tt) REVERT: B 202 GLN cc_start: 0.8504 (mt0) cc_final: 0.8120 (tt0) REVERT: B 204 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8270 (mt) REVERT: B 249 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 412 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (tp) REVERT: C 105 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6800 (mpm) REVERT: C 173 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: C 271 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8827 (tp) REVERT: D 63 SER cc_start: 0.8757 (t) cc_final: 0.8504 (p) REVERT: D 100 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: D 202 GLN cc_start: 0.8382 (mt0) cc_final: 0.8071 (mt0) REVERT: D 204 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8280 (mt) REVERT: D 412 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (tp) REVERT: E 49 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8224 (mmtt) REVERT: E 63 SER cc_start: 0.8695 (t) cc_final: 0.8453 (p) REVERT: E 133 LEU cc_start: 0.8514 (tp) cc_final: 0.8256 (tt) REVERT: E 139 ASN cc_start: 0.8612 (p0) cc_final: 0.8265 (p0) REVERT: E 159 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7986 (tmtt) REVERT: E 179 MET cc_start: 0.8656 (mmm) cc_final: 0.8252 (mmm) REVERT: E 249 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8060 (mp) outliers start: 102 outliers final: 53 residues processed: 425 average time/residue: 1.0741 time to fit residues: 505.7289 Evaluate side-chains 438 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 369 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 0.0040 chunk 96 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 47 ASN C 47 ASN C 202 GLN D 47 ASN E 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14500 Z= 0.182 Angle : 0.647 8.992 19680 Z= 0.318 Chirality : 0.045 0.157 2255 Planarity : 0.004 0.047 2435 Dihedral : 5.561 31.289 2200 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.16 % Allowed : 23.48 % Favored : 70.36 % 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: 0.87 (0.22), residues: 625 sheet: -0.41 (0.25), residues: 345 loop : -1.71 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 186 HIS 0.001 0.000 HIS E 125 PHE 0.016 0.001 PHE E 311 TYR 0.029 0.002 TYR E 317 ARG 0.005 0.000 ARG A 229 *********************** 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 510 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 416 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6777 (mpm) REVERT: A 139 ASN cc_start: 0.8633 (p0) cc_final: 0.8430 (p0) REVERT: A 173 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 242 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: A 395 PHE cc_start: 0.8761 (m-10) cc_final: 0.8534 (m-80) REVERT: B 97 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7737 (t0) REVERT: B 105 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6689 (mpm) REVERT: B 133 LEU cc_start: 0.8493 (tp) cc_final: 0.8237 (tt) REVERT: B 204 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8284 (mt) REVERT: C 105 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6815 (mpm) REVERT: C 120 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8376 (ttmt) REVERT: C 412 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8469 (tp) REVERT: C 424 THR cc_start: 0.9362 (m) cc_final: 0.9119 (m) REVERT: D 63 SER cc_start: 0.8792 (t) cc_final: 0.8541 (p) REVERT: D 100 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: D 179 MET cc_start: 0.8675 (mmm) cc_final: 0.8355 (mmm) REVERT: D 202 GLN cc_start: 0.8339 (mt0) cc_final: 0.8041 (mt0) REVERT: D 212 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7558 (ptt180) REVERT: D 227 GLU cc_start: 0.8573 (pt0) cc_final: 0.7344 (tt0) REVERT: D 229 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7572 (mtt-85) REVERT: D 412 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8444 (tp) REVERT: E 49 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8137 (mmtt) REVERT: E 63 SER cc_start: 0.8755 (t) cc_final: 0.8524 (p) REVERT: E 113 ASP cc_start: 0.8948 (p0) cc_final: 0.8695 (p0) REVERT: E 133 LEU cc_start: 0.8537 (tp) cc_final: 0.8295 (tt) REVERT: E 139 ASN cc_start: 0.8640 (p0) cc_final: 0.8272 (p0) REVERT: E 179 MET cc_start: 0.8650 (mmm) cc_final: 0.8276 (mmm) REVERT: E 204 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mt) REVERT: E 227 GLU cc_start: 0.8600 (pt0) cc_final: 0.8272 (tt0) outliers start: 94 outliers final: 48 residues processed: 437 average time/residue: 1.0743 time to fit residues: 520.8884 Evaluate side-chains 429 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 370 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 296 VAL 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: 0.4980 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 47 ASN C 47 ASN C 202 GLN D 47 ASN D 219 ASN E 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14500 Z= 0.201 Angle : 0.647 9.268 19680 Z= 0.319 Chirality : 0.045 0.192 2255 Planarity : 0.004 0.048 2435 Dihedral : 5.200 20.808 2200 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.70 % Allowed : 24.72 % Favored : 69.57 % 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: -0.60 (0.20), residues: 1710 helix: 1.01 (0.22), residues: 625 sheet: -0.34 (0.25), residues: 345 loop : -1.68 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 255 HIS 0.002 0.000 HIS E 125 PHE 0.021 0.001 PHE D 48 TYR 0.028 0.001 TYR E 317 ARG 0.007 0.000 ARG A 229 *********************** 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 474 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 387 time to evaluate : 2.356 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: A 105 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6730 (mpm) REVERT: A 173 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7051 (mt-10) REVERT: A 212 ARG cc_start: 0.8087 (ptp-170) cc_final: 0.7859 (ptp-170) REVERT: A 242 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 395 PHE cc_start: 0.8786 (m-10) cc_final: 0.8531 (m-80) REVERT: B 97 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 105 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6663 (mpm) REVERT: B 133 LEU cc_start: 0.8503 (tp) cc_final: 0.8245 (tt) REVERT: B 279 MET cc_start: 0.8751 (tpt) cc_final: 0.8545 (tpt) REVERT: C 105 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6769 (mpm) REVERT: C 120 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8361 (ttmt) REVERT: C 412 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8464 (tp) REVERT: C 424 THR cc_start: 0.9348 (m) cc_final: 0.9096 (m) REVERT: D 63 SER cc_start: 0.8791 (t) cc_final: 0.8532 (p) REVERT: D 212 ARG cc_start: 0.7986 (ptp-170) cc_final: 0.7525 (ptt180) REVERT: D 227 GLU cc_start: 0.8557 (pt0) cc_final: 0.7325 (tt0) REVERT: D 229 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7539 (mtt-85) REVERT: D 412 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (tp) REVERT: E 49 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8246 (mmtt) REVERT: E 63 SER cc_start: 0.8786 (t) cc_final: 0.8528 (p) REVERT: E 133 LEU cc_start: 0.8535 (tp) cc_final: 0.8305 (tt) REVERT: E 139 ASN cc_start: 0.8665 (p0) cc_final: 0.8385 (p0) REVERT: E 179 MET cc_start: 0.8633 (mmm) cc_final: 0.8272 (mmm) REVERT: E 204 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8339 (mt) outliers start: 87 outliers final: 53 residues processed: 413 average time/residue: 1.0434 time to fit residues: 477.7162 Evaluate side-chains 425 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 363 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.0040 chunk 149 optimal weight: 0.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 326 GLN C 47 ASN C 131 ASN C 202 GLN D 47 ASN D 131 ASN E 47 ASN E 62 ASN E 131 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14500 Z= 0.323 Angle : 0.692 8.623 19680 Z= 0.343 Chirality : 0.047 0.167 2255 Planarity : 0.004 0.048 2435 Dihedral : 5.249 21.409 2200 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.44 % Allowed : 25.64 % Favored : 68.92 % 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 (0.20), residues: 1710 helix: 1.12 (0.22), residues: 625 sheet: -0.35 (0.25), residues: 345 loop : -1.63 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 422 HIS 0.002 0.001 HIS E 217 PHE 0.020 0.002 PHE B 48 TYR 0.027 0.002 TYR C 317 ARG 0.005 0.000 ARG A 229 *********************** 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 463 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 380 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6776 (mpm) REVERT: A 212 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.7812 (ptp-170) REVERT: A 242 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 249 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 303 MET cc_start: 0.9243 (mmt) cc_final: 0.8982 (mmt) REVERT: A 395 PHE cc_start: 0.8795 (m-10) cc_final: 0.8520 (m-80) REVERT: B 105 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6692 (mpm) REVERT: B 133 LEU cc_start: 0.8548 (tp) cc_final: 0.8272 (tt) REVERT: B 139 ASN cc_start: 0.8610 (p0) cc_final: 0.8330 (p0) REVERT: B 249 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 412 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8563 (tp) REVERT: D 63 SER cc_start: 0.8758 (t) cc_final: 0.8462 (p) REVERT: D 212 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7808 (ptp-170) REVERT: D 227 GLU cc_start: 0.8584 (pt0) cc_final: 0.8371 (tt0) REVERT: D 412 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (tp) REVERT: E 49 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8337 (mmtt) REVERT: E 63 SER cc_start: 0.8758 (t) cc_final: 0.8510 (p) REVERT: E 133 LEU cc_start: 0.8571 (tp) cc_final: 0.8342 (tt) REVERT: E 139 ASN cc_start: 0.8663 (p0) cc_final: 0.8446 (p0) REVERT: E 159 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: E 179 MET cc_start: 0.8641 (mmm) cc_final: 0.8304 (mmm) outliers start: 83 outliers final: 55 residues processed: 407 average time/residue: 1.0566 time to fit residues: 477.7270 Evaluate side-chains 426 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 363 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 B 321 ASN C 47 ASN C 202 GLN D 47 ASN D 131 ASN E 47 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4598 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= 0.204 Angle : 0.676 9.197 19680 Z= 0.332 Chirality : 0.046 0.193 2255 Planarity : 0.004 0.048 2435 Dihedral : 5.142 22.127 2200 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.66 % Allowed : 26.16 % Favored : 69.18 % 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: -0.41 (0.20), residues: 1710 helix: 1.20 (0.22), residues: 625 sheet: -0.31 (0.25), residues: 345 loop : -1.56 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 422 HIS 0.001 0.000 HIS B 217 PHE 0.024 0.001 PHE A 48 TYR 0.029 0.002 TYR E 317 ARG 0.005 0.000 ARG A 229 *********************** 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: 71 poor density : 378 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6777 (mpm) REVERT: A 173 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 242 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 395 PHE cc_start: 0.8801 (m-10) cc_final: 0.8485 (m-80) REVERT: B 97 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7648 (t0) REVERT: B 105 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6643 (mpm) REVERT: B 133 LEU cc_start: 0.8510 (tp) cc_final: 0.8265 (tt) REVERT: B 139 ASN cc_start: 0.8608 (p0) cc_final: 0.8323 (p0) REVERT: C 412 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8493 (tp) REVERT: D 63 SER cc_start: 0.8797 (t) cc_final: 0.8547 (p) REVERT: D 94 TYR cc_start: 0.8057 (t80) cc_final: 0.7240 (t80) REVERT: D 249 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 412 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8508 (tp) REVERT: E 49 LYS cc_start: 0.8571 (mmtm) cc_final: 0.7869 (mmtt) REVERT: E 63 SER cc_start: 0.8796 (t) cc_final: 0.8542 (p) REVERT: E 133 LEU cc_start: 0.8522 (tp) cc_final: 0.8305 (tt) REVERT: E 179 MET cc_start: 0.8644 (mmm) cc_final: 0.8229 (mmm) REVERT: E 204 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8326 (mt) outliers start: 71 outliers final: 54 residues processed: 401 average time/residue: 1.0528 time to fit residues: 470.9548 Evaluate side-chains 424 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 362 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.0270 chunk 134 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 C 47 ASN C 202 GLN D 47 ASN D 62 ASN D 219 ASN E 47 ASN E 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14500 Z= 0.193 Angle : 0.684 9.919 19680 Z= 0.335 Chirality : 0.046 0.197 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.029 21.431 2200 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.33 % Allowed : 27.28 % Favored : 68.39 % 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: -0.45 (0.20), residues: 1710 helix: 1.12 (0.22), residues: 625 sheet: -0.24 (0.25), residues: 345 loop : -1.59 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.001 0.000 HIS B 125 PHE 0.021 0.001 PHE B 48 TYR 0.028 0.001 TYR C 317 ARG 0.005 0.000 ARG A 229 ********************** 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 445 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 379 time to evaluate : 1.634 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: A 105 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6715 (mpm) REVERT: A 173 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 242 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 395 PHE cc_start: 0.8803 (m-10) cc_final: 0.8488 (m-80) REVERT: B 97 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 105 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6619 (mpm) REVERT: B 133 LEU cc_start: 0.8513 (tp) cc_final: 0.8271 (tt) REVERT: B 139 ASN cc_start: 0.8642 (p0) cc_final: 0.8392 (p0) REVERT: C 164 ASP cc_start: 0.8474 (p0) cc_final: 0.8167 (p0) REVERT: D 63 SER cc_start: 0.8758 (t) cc_final: 0.8505 (p) REVERT: D 94 TYR cc_start: 0.8034 (t80) cc_final: 0.7437 (t80) REVERT: D 105 MET cc_start: 0.7384 (mmp) cc_final: 0.7155 (mmp) REVERT: E 63 SER cc_start: 0.8847 (t) cc_final: 0.8607 (p) REVERT: E 96 ASP cc_start: 0.8405 (t0) cc_final: 0.8200 (t0) REVERT: E 133 LEU cc_start: 0.8513 (tp) cc_final: 0.8285 (tt) REVERT: E 179 MET cc_start: 0.8636 (mmm) cc_final: 0.8238 (mmm) outliers start: 66 outliers final: 50 residues processed: 403 average time/residue: 1.0197 time to fit residues: 459.7004 Evaluate side-chains 421 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 367 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0070 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 C 202 GLN D 62 ASN E 47 ASN E 62 ASN E 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105046 restraints weight = 22019.880| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.94 r_work: 0.3088 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14500 Z= 0.188 Angle : 0.688 10.224 19680 Z= 0.335 Chirality : 0.046 0.189 2255 Planarity : 0.004 0.051 2435 Dihedral : 4.938 24.322 2200 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.85 % Allowed : 27.02 % Favored : 68.13 % 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: -0.42 (0.20), residues: 1710 helix: 1.10 (0.22), residues: 625 sheet: -0.13 (0.25), residues: 345 loop : -1.57 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 255 HIS 0.001 0.000 HIS E 125 PHE 0.037 0.001 PHE D 48 TYR 0.028 0.001 TYR C 317 ARG 0.005 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7446.65 seconds wall clock time: 133 minutes 3.56 seconds (7983.56 seconds total)