Starting phenix.real_space_refine on Sun Nov 17 08:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wge_37511/11_2024/8wge_37511.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 110 5.16 5 C 8765 2.51 5 N 2210 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13515 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.62, per 1000 atoms: 0.64 Number of scatterers: 13515 At special positions: 0 Unit cell: (86.1, 83.64, 155.8, 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 110 16.00 O 2430 8.00 N 2210 7.00 C 8765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 161 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A 501 " - " ASN A 132 " " NAG B 501 " - " ASN B 132 " " NAG C 501 " - " ASN C 132 " " NAG D 501 " - " ASN D 132 " " NAG E 501 " - " ASN E 132 " Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.8 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 22 sheets defined 42.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 4.054A pdb=" N GLU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 217 through 238 removed outlier: 5.015A pdb=" N LEU A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 308 Processing helix chain 'A' and resid 351 through 406 removed outlier: 3.601A pdb=" N VAL A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 4.032A pdb=" N GLU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 217 through 224 removed outlier: 3.631A pdb=" N MET B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.608A pdb=" N LEU B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 351 through 405 removed outlier: 3.654A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.942A pdb=" N GLU C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.599A pdb=" N MET C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.607A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 351 through 405 removed outlier: 3.610A pdb=" N VAL C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.989A pdb=" N GLU D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 217 through 224 removed outlier: 3.642A pdb=" N MET D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.607A pdb=" N LEU D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 351 through 405 removed outlier: 3.636A pdb=" N VAL D 356 " --> pdb=" O MET D 352 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.982A pdb=" N GLU E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 217 through 224 removed outlier: 3.562A pdb=" N MET E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 238 Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 248 through 268 removed outlier: 3.604A pdb=" N LEU E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.504A pdb=" N ARG E 303 " --> pdb=" O MET E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 405 removed outlier: 3.685A pdb=" N VAL E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.009A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 144 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 117 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.009A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 70 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 64 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 164 removed outlier: 7.241A pdb=" N PHE A 208 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU A 199 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 210 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 197 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 212 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 144 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER B 117 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 70 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 64 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 72 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 164 removed outlier: 7.230A pdb=" N PHE B 208 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 199 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 210 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 212 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 144 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER C 117 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG C 70 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL C 64 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN C 72 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 164 removed outlier: 7.285A pdb=" N PHE C 208 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 199 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 210 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA C 197 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY C 212 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 101 removed outlier: 7.990A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 144 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER D 117 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 101 removed outlier: 7.990A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 70 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL D 64 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN D 72 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'D' and resid 158 through 164 removed outlier: 7.243A pdb=" N PHE D 208 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU D 199 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA D 210 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA D 197 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY D 212 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.002A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 144 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER E 117 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.002A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG E 70 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN E 72 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC4, first strand: chain 'E' and resid 158 through 164 removed outlier: 7.207A pdb=" N PHE E 208 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU E 199 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA E 210 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA E 197 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY E 212 " --> pdb=" O THR E 195 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4280 1.34 - 1.46: 2916 1.46 - 1.58: 6419 1.58 - 1.69: 0 1.69 - 1.81: 175 Bond restraints: 13790 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 18184 1.04 - 2.07: 462 2.07 - 3.11: 109 3.11 - 4.15: 17 4.15 - 5.18: 18 Bond angle restraints: 18790 Sorted by residual: angle pdb=" N PRO E 155 " pdb=" CA PRO E 155 " pdb=" C PRO E 155 " ideal model delta sigma weight residual 112.10 116.50 -4.40 2.60e+00 1.48e-01 2.87e+00 angle pdb=" N VAL D 112 " pdb=" CA VAL D 112 " pdb=" C VAL D 112 " ideal model delta sigma weight residual 109.34 105.85 3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA PHE A 56 " pdb=" CB PHE A 56 " pdb=" CG PHE A 56 " ideal model delta sigma weight residual 113.80 115.47 -1.67 1.00e+00 1.00e+00 2.78e+00 angle pdb=" N VAL D 404 " pdb=" CA VAL D 404 " pdb=" C VAL D 404 " ideal model delta sigma weight residual 109.34 112.78 -3.44 2.08e+00 2.31e-01 2.74e+00 angle pdb=" N PRO B 155 " pdb=" CA PRO B 155 " pdb=" C PRO B 155 " ideal model delta sigma weight residual 112.10 116.40 -4.30 2.60e+00 1.48e-01 2.73e+00 ... (remaining 18785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7311 17.72 - 35.43: 771 35.43 - 53.15: 219 53.15 - 70.86: 19 70.86 - 88.58: 20 Dihedral angle restraints: 8340 sinusoidal: 3235 harmonic: 5105 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 161 " pdb=" CB CYS B 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS C 147 " pdb=" SG CYS C 147 " pdb=" SG CYS C 161 " pdb=" CB CYS C 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.41 -73.41 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 161 " pdb=" CB CYS E 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.36 -73.36 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1389 0.026 - 0.051: 551 0.051 - 0.077: 184 0.077 - 0.102: 85 0.102 - 0.128: 81 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE D 165 " pdb=" N ILE D 165 " pdb=" C ILE D 165 " pdb=" CB ILE D 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2287 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 56 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C PHE A 56 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 56 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 57 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 56 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C PHE C 56 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE C 56 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 57 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 154 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 155 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " -0.018 5.00e-02 4.00e+02 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3711 2.81 - 3.34: 12223 3.34 - 3.86: 22050 3.86 - 4.38: 25148 4.38 - 4.90: 45145 Nonbonded interactions: 108277 Sorted by model distance: nonbonded pdb=" NH2 ARG B 70 " pdb=" O LEU C 62 " model vdw 2.292 3.120 nonbonded pdb=" O THR A 175 " pdb=" OG1 THR A 175 " model vdw 2.300 3.040 nonbonded pdb=" O THR B 175 " pdb=" OG1 THR B 175 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG D 70 " pdb=" O LEU E 62 " model vdw 2.303 3.120 nonbonded pdb=" O THR D 175 " pdb=" OG1 THR D 175 " model vdw 2.304 3.040 ... (remaining 108272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.002 0.026 13790 Z= 0.139 Angle : 0.444 5.183 18790 Z= 0.218 Chirality : 0.039 0.128 2290 Planarity : 0.003 0.036 2345 Dihedral : 15.644 88.577 4990 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.34 % Allowed : 15.81 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.72 (0.21), residues: 1720 helix: 1.68 (0.19), residues: 695 sheet: 0.17 (0.25), residues: 495 loop : -0.73 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 192 HIS 0.008 0.000 HIS A 374 PHE 0.019 0.001 PHE E 385 TYR 0.012 0.001 TYR E 59 ARG 0.002 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 1.486 Fit side-chains REVERT: C 222 MET cc_start: 0.7598 (mtp) cc_final: 0.7312 (mtt) REVERT: D 56 PHE cc_start: 0.7568 (t80) cc_final: 0.7315 (t80) REVERT: D 222 MET cc_start: 0.7658 (mtp) cc_final: 0.7339 (mtt) outliers start: 5 outliers final: 1 residues processed: 241 average time/residue: 0.2395 time to fit residues: 86.0699 Evaluate side-chains 225 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS D 374 HIS E 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13790 Z= 0.388 Angle : 0.616 8.217 18790 Z= 0.310 Chirality : 0.045 0.147 2290 Planarity : 0.004 0.031 2345 Dihedral : 4.379 23.554 1953 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.64 % Allowed : 15.68 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.72 (0.21), residues: 1720 helix: 2.07 (0.19), residues: 690 sheet: -0.22 (0.24), residues: 520 loop : -0.90 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.017 0.002 PHE A 251 TYR 0.018 0.002 TYR D 406 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 1.669 Fit side-chains REVERT: A 56 PHE cc_start: 0.7730 (t80) cc_final: 0.7434 (t80) REVERT: B 33 MET cc_start: 0.7994 (ttp) cc_final: 0.7508 (ttm) REVERT: B 42 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7470 (ptm) REVERT: B 113 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8237 (ttpt) REVERT: C 222 MET cc_start: 0.7775 (mtp) cc_final: 0.7478 (mtt) REVERT: D 127 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8872 (pp) REVERT: E 259 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7691 (t80) REVERT: E 379 LYS cc_start: 0.7958 (mptt) cc_final: 0.7324 (ttpt) outliers start: 39 outliers final: 27 residues processed: 236 average time/residue: 0.2395 time to fit residues: 84.6308 Evaluate side-chains 239 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 374 HIS D 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13790 Z= 0.293 Angle : 0.560 7.776 18790 Z= 0.279 Chirality : 0.042 0.139 2290 Planarity : 0.004 0.029 2345 Dihedral : 4.079 16.833 1950 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 16.62 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1720 helix: 2.26 (0.19), residues: 685 sheet: -0.35 (0.24), residues: 520 loop : -0.85 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 PHE 0.014 0.002 PHE A 259 TYR 0.014 0.002 TYR B 406 ARG 0.002 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 1.512 Fit side-chains REVERT: A 56 PHE cc_start: 0.7454 (t80) cc_final: 0.7071 (t80) REVERT: B 33 MET cc_start: 0.8068 (ttp) cc_final: 0.7580 (ttm) REVERT: B 259 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 379 LYS cc_start: 0.8043 (mptt) cc_final: 0.7486 (ttpt) REVERT: C 222 MET cc_start: 0.7703 (mtp) cc_final: 0.7444 (mtt) REVERT: C 379 LYS cc_start: 0.7958 (mptt) cc_final: 0.7400 (ttpt) REVERT: D 56 PHE cc_start: 0.7461 (t80) cc_final: 0.7189 (t80) REVERT: D 127 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8868 (pp) REVERT: E 259 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7699 (t80) REVERT: E 379 LYS cc_start: 0.7913 (mptt) cc_final: 0.7327 (ttpt) REVERT: E 393 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7977 (mm) outliers start: 43 outliers final: 24 residues processed: 242 average time/residue: 0.2438 time to fit residues: 88.2229 Evaluate side-chains 237 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13790 Z= 0.425 Angle : 0.632 8.529 18790 Z= 0.314 Chirality : 0.045 0.147 2290 Planarity : 0.004 0.031 2345 Dihedral : 4.356 17.700 1950 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.45 % Allowed : 17.43 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.57 (0.20), residues: 1720 helix: 2.07 (0.19), residues: 685 sheet: -0.49 (0.24), residues: 510 loop : -0.91 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.018 0.002 PHE A 259 TYR 0.018 0.002 TYR D 406 ARG 0.003 0.000 ARG E 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.601 Fit side-chains REVERT: A 263 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7818 (tt) REVERT: B 42 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7653 (ptm) REVERT: B 259 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7666 (t80) REVERT: B 379 LYS cc_start: 0.8047 (mptt) cc_final: 0.7478 (ttpt) REVERT: C 379 LYS cc_start: 0.7877 (mptt) cc_final: 0.7366 (ttpt) REVERT: D 259 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7703 (t80) REVERT: D 379 LYS cc_start: 0.7966 (mptt) cc_final: 0.7385 (ttpt) REVERT: E 259 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7690 (t80) REVERT: E 379 LYS cc_start: 0.7918 (mptt) cc_final: 0.7325 (ttpt) outliers start: 51 outliers final: 34 residues processed: 244 average time/residue: 0.2547 time to fit residues: 92.0559 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS E 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13790 Z= 0.210 Angle : 0.520 10.129 18790 Z= 0.259 Chirality : 0.041 0.136 2290 Planarity : 0.003 0.028 2345 Dihedral : 3.929 15.384 1950 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.64 % Allowed : 18.85 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.84 (0.21), residues: 1720 helix: 2.44 (0.19), residues: 685 sheet: -0.49 (0.24), residues: 520 loop : -0.85 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 81 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.001 PHE C 384 TYR 0.013 0.001 TYR D 406 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 1.540 Fit side-chains REVERT: A 56 PHE cc_start: 0.7363 (t80) cc_final: 0.6915 (t80) REVERT: B 33 MET cc_start: 0.8023 (ttp) cc_final: 0.7580 (ttm) REVERT: B 42 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7452 (ptm) REVERT: B 259 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 379 LYS cc_start: 0.7924 (mptt) cc_final: 0.7435 (ttpt) REVERT: C 379 LYS cc_start: 0.7758 (mptt) cc_final: 0.7344 (ttpt) REVERT: D 56 PHE cc_start: 0.7374 (t80) cc_final: 0.7135 (t80) REVERT: D 259 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7684 (t80) REVERT: D 379 LYS cc_start: 0.7886 (mptt) cc_final: 0.7388 (ttpt) REVERT: E 259 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7671 (t80) REVERT: E 379 LYS cc_start: 0.7859 (mptt) cc_final: 0.7336 (ttpt) REVERT: E 393 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7972 (mm) outliers start: 39 outliers final: 27 residues processed: 254 average time/residue: 0.2361 time to fit residues: 90.6160 Evaluate side-chains 249 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13790 Z= 0.145 Angle : 0.480 9.276 18790 Z= 0.239 Chirality : 0.039 0.132 2290 Planarity : 0.003 0.028 2345 Dihedral : 3.638 13.068 1950 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 19.59 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.15 (0.21), residues: 1720 helix: 2.71 (0.19), residues: 695 sheet: -0.39 (0.24), residues: 525 loop : -0.68 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.002 0.001 HIS D 283 PHE 0.017 0.001 PHE B 384 TYR 0.015 0.001 TYR D 406 ARG 0.001 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.547 Fit side-chains REVERT: A 56 PHE cc_start: 0.7110 (t80) cc_final: 0.6811 (t80) REVERT: A 259 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7788 (t80) REVERT: B 33 MET cc_start: 0.7973 (ttp) cc_final: 0.7568 (ttm) REVERT: B 36 ASP cc_start: 0.7627 (m-30) cc_final: 0.7354 (m-30) REVERT: B 56 PHE cc_start: 0.7167 (t80) cc_final: 0.6958 (t80) REVERT: B 259 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7703 (t80) REVERT: B 379 LYS cc_start: 0.7880 (mptt) cc_final: 0.7523 (ttpt) REVERT: B 406 TYR cc_start: 0.7796 (t80) cc_final: 0.7460 (t80) REVERT: C 259 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 379 LYS cc_start: 0.7659 (mptt) cc_final: 0.7359 (ttpt) REVERT: D 259 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7794 (t80) REVERT: D 276 CYS cc_start: 0.6851 (m) cc_final: 0.6010 (p) REVERT: D 379 LYS cc_start: 0.7762 (mptt) cc_final: 0.7378 (ttpt) REVERT: D 393 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7722 (mt) REVERT: E 259 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7766 (t80) REVERT: E 393 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7958 (mm) outliers start: 37 outliers final: 16 residues processed: 248 average time/residue: 0.2181 time to fit residues: 83.9625 Evaluate side-chains 233 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13790 Z= 0.256 Angle : 0.536 9.140 18790 Z= 0.265 Chirality : 0.041 0.136 2290 Planarity : 0.004 0.030 2345 Dihedral : 3.899 15.493 1950 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.04 % Allowed : 19.93 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1720 helix: 2.66 (0.19), residues: 690 sheet: -0.49 (0.23), residues: 525 loop : -0.74 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 88 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.001 PHE A 251 TYR 0.021 0.002 TYR E 406 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 1.450 Fit side-chains REVERT: A 56 PHE cc_start: 0.7312 (t80) cc_final: 0.6875 (t80) REVERT: A 259 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (t80) REVERT: B 33 MET cc_start: 0.8074 (ttp) cc_final: 0.7611 (ttm) REVERT: B 42 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7411 (ptm) REVERT: B 127 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 259 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7670 (t80) REVERT: B 379 LYS cc_start: 0.7834 (mptt) cc_final: 0.7439 (ttpt) REVERT: C 263 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7981 (tt) REVERT: C 379 LYS cc_start: 0.7632 (mptt) cc_final: 0.7345 (ttpt) REVERT: D 259 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7747 (t80) REVERT: D 379 LYS cc_start: 0.7794 (mptt) cc_final: 0.7373 (ttpt) REVERT: E 259 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7710 (t80) REVERT: E 263 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8043 (tt) REVERT: E 379 LYS cc_start: 0.7781 (mptt) cc_final: 0.7358 (ttpt) REVERT: E 393 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (mm) outliers start: 45 outliers final: 26 residues processed: 238 average time/residue: 0.2493 time to fit residues: 88.5429 Evaluate side-chains 244 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13790 Z= 0.288 Angle : 0.563 9.759 18790 Z= 0.278 Chirality : 0.042 0.138 2290 Planarity : 0.004 0.037 2345 Dihedral : 4.031 15.929 1950 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.84 % Allowed : 20.47 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.87 (0.21), residues: 1720 helix: 2.47 (0.19), residues: 690 sheet: -0.56 (0.23), residues: 525 loop : -0.76 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 PHE 0.014 0.002 PHE A 251 TYR 0.022 0.002 TYR D 406 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.234 Fit side-chains REVERT: A 56 PHE cc_start: 0.7398 (t80) cc_final: 0.6895 (t80) REVERT: A 259 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 33 MET cc_start: 0.8099 (ttp) cc_final: 0.7618 (ttm) REVERT: B 42 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7390 (ptm) REVERT: B 259 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 379 LYS cc_start: 0.7858 (mptt) cc_final: 0.7445 (ttpt) REVERT: C 263 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7930 (tt) REVERT: C 379 LYS cc_start: 0.7669 (mptt) cc_final: 0.7360 (ttpt) REVERT: D 259 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7723 (t80) REVERT: D 263 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8117 (tt) REVERT: D 379 LYS cc_start: 0.7867 (mptt) cc_final: 0.7431 (ttpt) REVERT: E 259 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7700 (t80) REVERT: E 263 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8029 (tt) REVERT: E 379 LYS cc_start: 0.7808 (mptt) cc_final: 0.7370 (ttpt) outliers start: 42 outliers final: 29 residues processed: 230 average time/residue: 0.2608 time to fit residues: 89.6784 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13790 Z= 0.226 Angle : 0.533 10.129 18790 Z= 0.265 Chirality : 0.041 0.136 2290 Planarity : 0.004 0.034 2345 Dihedral : 3.925 15.217 1950 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.77 % Allowed : 20.61 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.97 (0.21), residues: 1720 helix: 2.59 (0.19), residues: 690 sheet: -0.54 (0.23), residues: 525 loop : -0.71 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 88 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.001 PHE E 384 TYR 0.018 0.001 TYR E 406 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 1.623 Fit side-chains REVERT: A 56 PHE cc_start: 0.7302 (t80) cc_final: 0.6895 (t80) REVERT: A 259 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 33 MET cc_start: 0.8067 (ttp) cc_final: 0.7613 (ttm) REVERT: B 259 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7685 (t80) REVERT: B 263 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 379 LYS cc_start: 0.7824 (mptt) cc_final: 0.7432 (ttpt) REVERT: C 263 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8009 (tt) REVERT: C 379 LYS cc_start: 0.7635 (mptt) cc_final: 0.7355 (ttpt) REVERT: D 259 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 263 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8141 (tt) REVERT: D 379 LYS cc_start: 0.7826 (mptt) cc_final: 0.7395 (ttpt) REVERT: E 259 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7659 (t80) REVERT: E 263 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8051 (tt) REVERT: E 379 LYS cc_start: 0.7808 (mptt) cc_final: 0.7377 (ttpt) REVERT: E 393 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8040 (mm) outliers start: 41 outliers final: 24 residues processed: 237 average time/residue: 0.2345 time to fit residues: 84.0269 Evaluate side-chains 241 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 112 optimal weight: 0.0470 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13790 Z= 0.247 Angle : 0.546 9.921 18790 Z= 0.271 Chirality : 0.042 0.137 2290 Planarity : 0.004 0.033 2345 Dihedral : 3.979 15.636 1950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.43 % Allowed : 20.95 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.93 (0.21), residues: 1720 helix: 2.55 (0.19), residues: 690 sheet: -0.58 (0.23), residues: 525 loop : -0.71 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 PHE 0.014 0.001 PHE E 384 TYR 0.022 0.002 TYR B 406 ARG 0.002 0.000 ARG D 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.588 Fit side-chains REVERT: A 56 PHE cc_start: 0.7317 (t80) cc_final: 0.6879 (t80) REVERT: A 259 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7854 (t80) REVERT: B 33 MET cc_start: 0.8079 (ttp) cc_final: 0.7619 (ttm) REVERT: B 259 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 263 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7921 (tt) REVERT: B 379 LYS cc_start: 0.7822 (mptt) cc_final: 0.7429 (ttpt) REVERT: C 263 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 379 LYS cc_start: 0.7632 (mptt) cc_final: 0.7355 (ttpt) REVERT: D 259 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7708 (t80) REVERT: D 263 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 379 LYS cc_start: 0.7823 (mptt) cc_final: 0.7395 (ttpt) REVERT: D 399 MET cc_start: 0.8466 (tpp) cc_final: 0.8178 (tpt) REVERT: E 259 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7680 (t80) REVERT: E 263 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8051 (tt) REVERT: E 379 LYS cc_start: 0.7799 (mptt) cc_final: 0.7367 (ttpt) REVERT: E 393 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8050 (mm) outliers start: 36 outliers final: 23 residues processed: 232 average time/residue: 0.2427 time to fit residues: 83.8340 Evaluate side-chains 242 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 ASN E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102755 restraints weight = 15566.575| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.69 r_work: 0.2896 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13790 Z= 0.161 Angle : 0.500 9.325 18790 Z= 0.251 Chirality : 0.040 0.131 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.710 13.103 1950 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 21.28 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1720 helix: 2.77 (0.19), residues: 695 sheet: -0.49 (0.24), residues: 525 loop : -0.56 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.002 0.001 HIS A 283 PHE 0.016 0.001 PHE C 384 TYR 0.019 0.001 TYR B 406 ARG 0.002 0.000 ARG E 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.85 seconds wall clock time: 51 minutes 38.74 seconds (3098.74 seconds total)