Starting phenix.real_space_refine on Fri Feb 16 16:20:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uzz_20965/02_2024/6uzz_20965.pdb" } resolution = 3.1 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 80 5.16 5 C 10196 2.51 5 N 2708 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 228": "NH1" <-> "NH2" Residue "E ARG 237": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Residue "E ARG 507": "NH1" <-> "NH2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E ARG 539": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "G ARG 507": "NH1" <-> "NH2" Residue "G ARG 511": "NH1" <-> "NH2" Residue "G ARG 539": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15832 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 Time building chain proxies: 8.56, per 1000 atoms: 0.54 Number of scatterers: 15832 At special positions: 0 Unit cell: (112.27, 112.27, 125.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 80 16.00 O 2840 8.00 N 2708 7.00 C 10196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 78.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.279A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.854A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.595A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 337 through 358 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.393A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.677A pdb=" N GLU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN B 112 " --> pdb=" O HIS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.656A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.280A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL C 241 " --> pdb=" O MET C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 337 through 358 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.679A pdb=" N GLU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.279A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL E 241 " --> pdb=" O MET E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 337 through 358 Proline residue: E 343 - end of helix Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 363 through 366 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.678A pdb=" N GLU F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 150 through 155 Processing helix chain 'G' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.280A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 233 " --> pdb=" O GLY G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA G 302 " --> pdb=" O SER G 298 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 337 through 358 Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 567 removed outlier: 3.714A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.676A pdb=" N LEU H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.679A pdb=" N GLU H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN H 112 " --> pdb=" O HIS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1045 hydrogen bonds defined for protein. 3111 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: 4.59 Time building geometry restraints manager: 6.91 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: 5043 1.34 - 1.45: 2602 1.45 - 1.57: 8371 1.57 - 1.69: 0 1.69 - 1.80: 136 Bond restraints: 16152 Sorted by residual: bond pdb=" CG LEU H 117 " pdb=" CD1 LEU H 117 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CG LEU B 117 " pdb=" CD1 LEU B 117 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" CG LEU D 117 " pdb=" CD1 LEU D 117 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CG LEU F 117 " pdb=" CD1 LEU F 117 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 bond pdb=" CG LEU C 273 " pdb=" CD1 LEU C 273 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.81e+00 ... (remaining 16147 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.83: 320 106.83 - 113.66: 8927 113.66 - 120.49: 7323 120.49 - 127.31: 5098 127.31 - 134.14: 156 Bond angle restraints: 21824 Sorted by residual: angle pdb=" C LYS B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LYS H 95 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LYS F 95 " pdb=" N ASP F 96 " pdb=" CA ASP F 96 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C LYS D 95 " pdb=" N ASP D 96 " pdb=" CA ASP D 96 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 angle pdb=" N LEU G 342 " pdb=" CA LEU G 342 " pdb=" C LEU G 342 " ideal model delta sigma weight residual 109.81 118.20 -8.39 2.21e+00 2.05e-01 1.44e+01 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 8814 14.17 - 28.33: 488 28.33 - 42.50: 158 42.50 - 56.67: 16 56.67 - 70.83: 16 Dihedral angle restraints: 9492 sinusoidal: 3776 harmonic: 5716 Sorted by residual: dihedral pdb=" CA ARG H 75 " pdb=" C ARG H 75 " pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ARG B 75 " pdb=" C ARG B 75 " pdb=" N LYS B 76 " pdb=" CA LYS B 76 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N LYS D 76 " pdb=" CA LYS D 76 " ideal model delta harmonic sigma weight residual 180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1537 0.048 - 0.095: 672 0.095 - 0.143: 184 0.143 - 0.190: 39 0.190 - 0.238: 12 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CB ILE C 337 " pdb=" CA ILE C 337 " pdb=" CG1 ILE C 337 " pdb=" CG2 ILE C 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 337 " pdb=" CA ILE G 337 " pdb=" CG1 ILE G 337 " pdb=" CG2 ILE G 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE A 337 " pdb=" CA ILE A 337 " pdb=" CG1 ILE A 337 " pdb=" CG2 ILE A 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2441 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 351 " -0.024 2.00e-02 2.50e+03 2.07e-02 7.48e+00 pdb=" CG PHE G 351 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE G 351 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE G 351 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE G 351 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 351 " -0.024 2.00e-02 2.50e+03 2.06e-02 7.40e+00 pdb=" CG PHE A 351 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 351 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 351 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 351 " 0.024 2.00e-02 2.50e+03 2.05e-02 7.38e+00 pdb=" CG PHE C 351 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 351 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 351 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 351 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 351 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 351 " 0.003 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5249 2.84 - 3.36: 14813 3.36 - 3.87: 25316 3.87 - 4.39: 28496 4.39 - 4.90: 49558 Nonbonded interactions: 123432 Sorted by model distance: nonbonded pdb=" OH TYR A 522 " pdb=" OG SER B 82 " model vdw 2.325 2.440 nonbonded pdb=" OE2 GLU A 284 " pdb=" OG1 THR A 322 " model vdw 2.357 2.440 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 322 " model vdw 2.357 2.440 nonbonded pdb=" OE2 GLU C 284 " pdb=" OG1 THR C 322 " model vdw 2.357 2.440 nonbonded pdb=" OE2 GLU E 284 " pdb=" OG1 THR E 322 " model vdw 2.357 2.440 ... (remaining 123427 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.83 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: 1.160 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: 0.020 Extract box with map and model: 6.700 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.450 Find NCS groups from input model: 1.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.009 0.069 16152 Z= 0.591 Angle : 0.922 9.536 21824 Z= 0.509 Chirality : 0.057 0.238 2444 Planarity : 0.006 0.050 2752 Dihedral : 10.608 70.833 5812 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.95 % Rotamer: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % 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: -4.22 (0.13), residues: 1952 helix: -2.92 (0.08), residues: 1504 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 379 HIS 0.006 0.001 HIS E 105 PHE 0.048 0.003 PHE G 351 TYR 0.025 0.003 TYR C 299 ARG 0.011 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 372 time to evaluate : 2.206 Fit side-chains REVERT: A 147 GLN cc_start: 0.8310 (mt0) cc_final: 0.7898 (mt0) REVERT: A 195 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8143 (ttm170) REVERT: A 228 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7659 (tmt170) REVERT: A 261 GLU cc_start: 0.8618 (mp0) cc_final: 0.8356 (mp0) REVERT: A 527 LYS cc_start: 0.7897 (tmmt) cc_final: 0.6965 (ttmt) REVERT: A 539 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7470 (ttm110) REVERT: A 543 GLU cc_start: 0.7840 (tt0) cc_final: 0.7623 (mt-10) REVERT: A 546 SER cc_start: 0.8755 (t) cc_final: 0.8340 (m) REVERT: A 562 ARG cc_start: 0.7329 (ttm170) cc_final: 0.7041 (tmt-80) REVERT: B 15 GLU cc_start: 0.8450 (tp30) cc_final: 0.8136 (tp30) REVERT: B 43 ASN cc_start: 0.8536 (t0) cc_final: 0.8322 (t0) REVERT: B 54 ASN cc_start: 0.8418 (m110) cc_final: 0.8049 (m110) REVERT: B 83 GLU cc_start: 0.7607 (tt0) cc_final: 0.7235 (mt-10) REVERT: B 117 LEU cc_start: 0.7281 (mp) cc_final: 0.6924 (mp) REVERT: C 147 GLN cc_start: 0.8306 (mt0) cc_final: 0.7891 (mt0) REVERT: C 195 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8137 (ttm170) REVERT: C 228 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7663 (tmt170) REVERT: C 261 GLU cc_start: 0.8611 (mp0) cc_final: 0.8344 (mp0) REVERT: C 527 LYS cc_start: 0.7907 (tmmt) cc_final: 0.6976 (ttmt) REVERT: C 539 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7477 (ttm110) REVERT: C 543 GLU cc_start: 0.7837 (tt0) cc_final: 0.7618 (mt-10) REVERT: C 546 SER cc_start: 0.8744 (t) cc_final: 0.8324 (m) REVERT: C 562 ARG cc_start: 0.7325 (ttm170) cc_final: 0.7039 (tmt-80) REVERT: D 15 GLU cc_start: 0.8439 (tp30) cc_final: 0.8138 (tp30) REVERT: D 54 ASN cc_start: 0.8480 (m110) cc_final: 0.8152 (m110) REVERT: D 83 GLU cc_start: 0.7600 (tt0) cc_final: 0.7220 (mt-10) REVERT: D 117 LEU cc_start: 0.7529 (mp) cc_final: 0.7029 (mp) REVERT: D 144 GLN cc_start: 0.8668 (mm110) cc_final: 0.8387 (mm-40) REVERT: E 147 GLN cc_start: 0.8313 (mt0) cc_final: 0.7896 (mt0) REVERT: E 195 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8139 (ttm170) REVERT: E 228 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7668 (tmt170) REVERT: E 261 GLU cc_start: 0.8616 (mp0) cc_final: 0.8355 (mp0) REVERT: E 527 LYS cc_start: 0.7895 (tmmt) cc_final: 0.6963 (ttmt) REVERT: E 539 ARG cc_start: 0.8003 (ttt-90) cc_final: 0.7479 (ttm110) REVERT: E 543 GLU cc_start: 0.7857 (tt0) cc_final: 0.7635 (mt-10) REVERT: E 546 SER cc_start: 0.8747 (t) cc_final: 0.8327 (m) REVERT: E 562 ARG cc_start: 0.7349 (ttm170) cc_final: 0.7057 (tmt-80) REVERT: F 15 GLU cc_start: 0.8439 (tp30) cc_final: 0.8138 (tp30) REVERT: F 54 ASN cc_start: 0.8460 (m110) cc_final: 0.8126 (m110) REVERT: F 83 GLU cc_start: 0.7567 (tt0) cc_final: 0.7258 (mt-10) REVERT: F 117 LEU cc_start: 0.7536 (mp) cc_final: 0.7032 (mp) REVERT: F 144 GLN cc_start: 0.8663 (mm110) cc_final: 0.8402 (mm-40) REVERT: G 147 GLN cc_start: 0.8316 (mt0) cc_final: 0.7903 (mt0) REVERT: G 195 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8138 (ttm170) REVERT: G 228 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7710 (tmt170) REVERT: G 260 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7438 (tt0) REVERT: G 261 GLU cc_start: 0.8614 (mp0) cc_final: 0.8349 (mp0) REVERT: G 527 LYS cc_start: 0.7889 (tmmt) cc_final: 0.6958 (ttmt) REVERT: G 539 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7480 (ttm110) REVERT: G 543 GLU cc_start: 0.7840 (tt0) cc_final: 0.7622 (mt-10) REVERT: G 546 SER cc_start: 0.8748 (t) cc_final: 0.8330 (m) REVERT: G 562 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7030 (tmt-80) REVERT: H 15 GLU cc_start: 0.8440 (tp30) cc_final: 0.8141 (tp30) REVERT: H 54 ASN cc_start: 0.8459 (m110) cc_final: 0.8120 (m110) REVERT: H 83 GLU cc_start: 0.7573 (tt0) cc_final: 0.7260 (mt-10) REVERT: H 117 LEU cc_start: 0.7537 (mp) cc_final: 0.7032 (mp) REVERT: H 144 GLN cc_start: 0.8671 (mm110) cc_final: 0.8415 (mm-40) outliers start: 4 outliers final: 0 residues processed: 376 average time/residue: 0.3960 time to fit residues: 201.4195 Evaluate side-chains 246 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.0470 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 357 GLN A 386 ASN A 560 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS C 357 GLN C 386 ASN C 560 GLN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 HIS E 357 GLN E 386 ASN E 560 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 HIS G 357 GLN G 386 ASN G 560 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16152 Z= 0.155 Angle : 0.489 5.694 21824 Z= 0.264 Chirality : 0.037 0.116 2444 Planarity : 0.004 0.025 2752 Dihedral : 4.068 17.814 2164 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.20 % Allowed : 7.77 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 1952 helix: -0.04 (0.12), residues: 1508 sheet: None (None), residues: 0 loop : -0.71 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 379 HIS 0.003 0.001 HIS A 105 PHE 0.019 0.001 PHE A 351 TYR 0.010 0.001 TYR E 299 ARG 0.003 0.000 ARG E 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 321 time to evaluate : 1.931 Fit side-chains REVERT: A 147 GLN cc_start: 0.7914 (mt0) cc_final: 0.7597 (mt0) REVERT: A 157 PHE cc_start: 0.7525 (t80) cc_final: 0.6992 (t80) REVERT: A 195 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.8156 (ttm170) REVERT: A 228 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7476 (tmt170) REVERT: A 238 MET cc_start: 0.8495 (tpp) cc_final: 0.7956 (mmt) REVERT: A 527 LYS cc_start: 0.7854 (tmmt) cc_final: 0.6920 (ttmt) REVERT: A 546 SER cc_start: 0.8528 (t) cc_final: 0.8093 (m) REVERT: A 560 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7066 (tp-100) REVERT: B 23 ASP cc_start: 0.4215 (OUTLIER) cc_final: 0.3860 (p0) REVERT: B 42 GLN cc_start: 0.8635 (mm110) cc_final: 0.8207 (mm-40) REVERT: B 54 ASN cc_start: 0.8180 (m110) cc_final: 0.7727 (m110) REVERT: B 105 GLU cc_start: 0.7378 (tp30) cc_final: 0.7047 (tt0) REVERT: B 118 THR cc_start: 0.8078 (m) cc_final: 0.7698 (p) REVERT: C 147 GLN cc_start: 0.7910 (mt0) cc_final: 0.7593 (mt0) REVERT: C 157 PHE cc_start: 0.7473 (t80) cc_final: 0.6950 (t80) REVERT: C 195 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8172 (ttm170) REVERT: C 228 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7480 (tmt170) REVERT: C 238 MET cc_start: 0.8497 (tpp) cc_final: 0.7954 (mmt) REVERT: C 527 LYS cc_start: 0.7829 (tmmt) cc_final: 0.6885 (ttmt) REVERT: C 546 SER cc_start: 0.8517 (t) cc_final: 0.8086 (m) REVERT: C 560 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7432 (tp40) REVERT: D 54 ASN cc_start: 0.8266 (m110) cc_final: 0.7749 (m110) REVERT: D 117 LEU cc_start: 0.7657 (mp) cc_final: 0.7308 (mp) REVERT: D 118 THR cc_start: 0.7922 (m) cc_final: 0.7530 (p) REVERT: E 147 GLN cc_start: 0.7917 (mt0) cc_final: 0.7601 (mt0) REVERT: E 157 PHE cc_start: 0.7504 (t80) cc_final: 0.6975 (t80) REVERT: E 195 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8170 (ttm170) REVERT: E 228 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7483 (tmt170) REVERT: E 238 MET cc_start: 0.8495 (tpp) cc_final: 0.7953 (mmt) REVERT: E 527 LYS cc_start: 0.7834 (tmmt) cc_final: 0.7157 (tmmt) REVERT: E 546 SER cc_start: 0.8520 (t) cc_final: 0.8089 (m) REVERT: E 560 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7436 (tp40) REVERT: F 42 GLN cc_start: 0.8551 (mm110) cc_final: 0.8344 (mm110) REVERT: F 54 ASN cc_start: 0.8247 (m110) cc_final: 0.7729 (m110) REVERT: F 117 LEU cc_start: 0.7653 (mp) cc_final: 0.7291 (mp) REVERT: F 118 THR cc_start: 0.7855 (m) cc_final: 0.7458 (p) REVERT: F 138 ASN cc_start: 0.7320 (t0) cc_final: 0.6936 (t0) REVERT: F 140 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: G 147 GLN cc_start: 0.7921 (mt0) cc_final: 0.7600 (mt0) REVERT: G 195 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.8170 (ttm170) REVERT: G 228 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7486 (tmt170) REVERT: G 238 MET cc_start: 0.8493 (tpp) cc_final: 0.7949 (mmt) REVERT: G 527 LYS cc_start: 0.7831 (tmmt) cc_final: 0.6887 (ttmt) REVERT: G 546 SER cc_start: 0.8522 (t) cc_final: 0.8091 (m) REVERT: G 560 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7418 (tp40) REVERT: H 54 ASN cc_start: 0.8243 (m110) cc_final: 0.7738 (m110) REVERT: H 117 LEU cc_start: 0.7663 (mp) cc_final: 0.7308 (mp) REVERT: H 118 THR cc_start: 0.7882 (m) cc_final: 0.7469 (p) outliers start: 20 outliers final: 13 residues processed: 333 average time/residue: 0.3375 time to fit residues: 156.1557 Evaluate side-chains 261 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 554 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 176 optimal weight: 0.0060 chunk 60 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 overall best weight: 2.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 549 HIS A 560 GLN C 357 GLN C 549 HIS C 560 GLN D 42 GLN E 357 GLN E 549 HIS E 560 GLN F 112 ASN G 357 GLN G 549 HIS G 560 GLN H 42 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16152 Z= 0.325 Angle : 0.553 5.798 21824 Z= 0.293 Chirality : 0.041 0.151 2444 Planarity : 0.004 0.044 2752 Dihedral : 4.020 18.043 2164 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 9.64 % Favored : 87.59 % 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: 0.86 (0.18), residues: 1952 helix: 0.96 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -0.54 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 379 HIS 0.003 0.001 HIS E 258 PHE 0.016 0.001 PHE G 351 TYR 0.017 0.002 TYR A 545 ARG 0.005 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.880 Fit side-chains REVERT: A 147 GLN cc_start: 0.7958 (mt0) cc_final: 0.7690 (mt0) REVERT: A 228 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7468 (tmt170) REVERT: A 357 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: A 527 LYS cc_start: 0.7756 (tmmt) cc_final: 0.6931 (ttmt) REVERT: A 546 SER cc_start: 0.8588 (t) cc_final: 0.7977 (m) REVERT: A 553 MET cc_start: 0.8328 (mmm) cc_final: 0.8083 (mmm) REVERT: A 560 GLN cc_start: 0.7810 (tp40) cc_final: 0.7245 (tp40) REVERT: B 42 GLN cc_start: 0.8590 (mm110) cc_final: 0.8226 (mm-40) REVERT: B 54 ASN cc_start: 0.8268 (m110) cc_final: 0.7913 (m110) REVERT: B 105 GLU cc_start: 0.7402 (tp30) cc_final: 0.7062 (tt0) REVERT: C 147 GLN cc_start: 0.7954 (mt0) cc_final: 0.7686 (mt0) REVERT: C 228 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7475 (tmt170) REVERT: C 357 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: C 527 LYS cc_start: 0.7752 (tmmt) cc_final: 0.6928 (ttmt) REVERT: C 546 SER cc_start: 0.8578 (t) cc_final: 0.7967 (m) REVERT: C 553 MET cc_start: 0.8328 (mmm) cc_final: 0.8084 (mmm) REVERT: C 560 GLN cc_start: 0.7806 (tp40) cc_final: 0.7239 (tp40) REVERT: D 42 GLN cc_start: 0.8648 (mm110) cc_final: 0.8302 (mm110) REVERT: D 54 ASN cc_start: 0.8254 (m110) cc_final: 0.7897 (m110) REVERT: D 117 LEU cc_start: 0.7892 (mp) cc_final: 0.7684 (mt) REVERT: E 147 GLN cc_start: 0.7962 (mt0) cc_final: 0.7691 (mt0) REVERT: E 228 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7478 (tmt170) REVERT: E 357 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: E 527 LYS cc_start: 0.7754 (tmmt) cc_final: 0.6929 (ttmt) REVERT: E 546 SER cc_start: 0.8581 (t) cc_final: 0.7970 (m) REVERT: E 553 MET cc_start: 0.8324 (mmm) cc_final: 0.8085 (mmm) REVERT: E 560 GLN cc_start: 0.7811 (tp40) cc_final: 0.7245 (tp40) REVERT: F 54 ASN cc_start: 0.8255 (m110) cc_final: 0.7898 (m110) REVERT: F 117 LEU cc_start: 0.7891 (mp) cc_final: 0.7682 (mt) REVERT: G 147 GLN cc_start: 0.7958 (mt0) cc_final: 0.7685 (mt0) REVERT: G 228 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7503 (tmt170) REVERT: G 357 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (tp40) REVERT: G 527 LYS cc_start: 0.7753 (tmmt) cc_final: 0.6930 (ttmt) REVERT: G 546 SER cc_start: 0.8585 (t) cc_final: 0.7976 (m) REVERT: G 553 MET cc_start: 0.8328 (mmm) cc_final: 0.8088 (mmm) REVERT: G 560 GLN cc_start: 0.7816 (tp40) cc_final: 0.7249 (tp40) REVERT: H 42 GLN cc_start: 0.8643 (mm110) cc_final: 0.8297 (mm110) REVERT: H 54 ASN cc_start: 0.8256 (m110) cc_final: 0.7899 (m110) REVERT: H 117 LEU cc_start: 0.7897 (mp) cc_final: 0.7689 (mt) outliers start: 46 outliers final: 38 residues processed: 259 average time/residue: 0.3232 time to fit residues: 117.7823 Evaluate side-chains 261 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 119 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN F 42 GLN G 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16152 Z= 0.168 Angle : 0.456 6.261 21824 Z= 0.239 Chirality : 0.037 0.118 2444 Planarity : 0.003 0.021 2752 Dihedral : 3.681 16.419 2164 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.35 % Allowed : 12.05 % Favored : 85.60 % 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: 1.80 (0.19), residues: 1952 helix: 1.63 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.22 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.002 0.001 HIS G 258 PHE 0.012 0.001 PHE E 351 TYR 0.011 0.001 TYR A 545 ARG 0.003 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 3.568 Fit side-chains REVERT: A 147 GLN cc_start: 0.7906 (mt0) cc_final: 0.7659 (mt0) REVERT: A 228 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7436 (tmt170) REVERT: A 238 MET cc_start: 0.8418 (tpp) cc_final: 0.7974 (mmt) REVERT: A 357 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7577 (tp40) REVERT: A 527 LYS cc_start: 0.7734 (tmmt) cc_final: 0.6904 (ttmt) REVERT: A 546 SER cc_start: 0.8589 (t) cc_final: 0.8072 (m) REVERT: A 560 GLN cc_start: 0.7764 (tp40) cc_final: 0.7219 (tp40) REVERT: B 23 ASP cc_start: 0.5021 (OUTLIER) cc_final: 0.4020 (p0) REVERT: B 54 ASN cc_start: 0.8224 (m110) cc_final: 0.7840 (m110) REVERT: B 105 GLU cc_start: 0.7294 (tp30) cc_final: 0.6971 (tt0) REVERT: C 147 GLN cc_start: 0.7901 (mt0) cc_final: 0.7653 (mt0) REVERT: C 228 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7444 (tmt170) REVERT: C 238 MET cc_start: 0.8446 (tpp) cc_final: 0.8016 (mmt) REVERT: C 357 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: C 527 LYS cc_start: 0.7731 (tmmt) cc_final: 0.6902 (ttmt) REVERT: C 546 SER cc_start: 0.8579 (t) cc_final: 0.8062 (m) REVERT: C 560 GLN cc_start: 0.7770 (tp40) cc_final: 0.7215 (tp40) REVERT: D 42 GLN cc_start: 0.8648 (mm110) cc_final: 0.8372 (mm-40) REVERT: D 54 ASN cc_start: 0.8235 (m110) cc_final: 0.7859 (m110) REVERT: D 117 LEU cc_start: 0.7895 (mp) cc_final: 0.7675 (mt) REVERT: E 147 GLN cc_start: 0.7908 (mt0) cc_final: 0.7661 (mt0) REVERT: E 228 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7446 (tmt170) REVERT: E 238 MET cc_start: 0.8444 (tpp) cc_final: 0.8015 (mmt) REVERT: E 357 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: E 527 LYS cc_start: 0.7727 (tmmt) cc_final: 0.6911 (ttmt) REVERT: E 546 SER cc_start: 0.8584 (t) cc_final: 0.8066 (m) REVERT: E 560 GLN cc_start: 0.7775 (tp40) cc_final: 0.7224 (tp40) REVERT: F 54 ASN cc_start: 0.8237 (m110) cc_final: 0.7860 (m110) REVERT: F 117 LEU cc_start: 0.7895 (mp) cc_final: 0.7647 (mt) REVERT: G 136 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7756 (m) REVERT: G 147 GLN cc_start: 0.7898 (mt0) cc_final: 0.7628 (mt0) REVERT: G 228 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7446 (tmt170) REVERT: G 238 MET cc_start: 0.8441 (tpp) cc_final: 0.8011 (mmt) REVERT: G 357 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7575 (tp40) REVERT: G 527 LYS cc_start: 0.7726 (tmmt) cc_final: 0.6911 (ttmt) REVERT: G 546 SER cc_start: 0.8585 (t) cc_final: 0.8069 (m) REVERT: G 560 GLN cc_start: 0.7779 (tp40) cc_final: 0.7225 (tp40) REVERT: H 42 GLN cc_start: 0.8640 (mm110) cc_final: 0.8357 (mm-40) REVERT: H 54 ASN cc_start: 0.8240 (m110) cc_final: 0.7863 (m110) REVERT: H 117 LEU cc_start: 0.7897 (mp) cc_final: 0.7650 (mt) outliers start: 39 outliers final: 18 residues processed: 275 average time/residue: 0.3349 time to fit residues: 131.4822 Evaluate side-chains 265 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.0030 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16152 Z= 0.144 Angle : 0.433 6.811 21824 Z= 0.226 Chirality : 0.037 0.114 2444 Planarity : 0.002 0.021 2752 Dihedral : 3.502 15.382 2164 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.93 % Allowed : 14.04 % Favored : 84.04 % 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: 2.32 (0.19), residues: 1952 helix: 2.01 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.07 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 379 HIS 0.002 0.001 HIS G 258 PHE 0.010 0.001 PHE A 351 TYR 0.010 0.001 TYR A 545 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 1.932 Fit side-chains REVERT: A 147 GLN cc_start: 0.7948 (mt0) cc_final: 0.7640 (mt0) REVERT: A 228 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7422 (tmt170) REVERT: A 238 MET cc_start: 0.8432 (tpp) cc_final: 0.8035 (mmt) REVERT: A 357 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7531 (tp40) REVERT: A 527 LYS cc_start: 0.7721 (tmmt) cc_final: 0.6878 (ttmt) REVERT: A 546 SER cc_start: 0.8569 (t) cc_final: 0.8048 (m) REVERT: A 560 GLN cc_start: 0.7747 (tp40) cc_final: 0.7217 (tp40) REVERT: B 23 ASP cc_start: 0.4970 (OUTLIER) cc_final: 0.3966 (p0) REVERT: B 43 ASN cc_start: 0.8473 (t0) cc_final: 0.8243 (t0) REVERT: B 45 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7090 (t) REVERT: B 54 ASN cc_start: 0.8190 (m110) cc_final: 0.7576 (m110) REVERT: B 105 GLU cc_start: 0.7279 (tp30) cc_final: 0.6971 (tt0) REVERT: C 147 GLN cc_start: 0.7941 (mt0) cc_final: 0.7634 (mt0) REVERT: C 228 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7378 (tmt170) REVERT: C 238 MET cc_start: 0.8401 (tpp) cc_final: 0.8007 (mmt) REVERT: C 357 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (tp40) REVERT: C 527 LYS cc_start: 0.7716 (tmmt) cc_final: 0.6873 (ttmt) REVERT: C 546 SER cc_start: 0.8562 (t) cc_final: 0.8038 (m) REVERT: C 560 GLN cc_start: 0.7744 (tp40) cc_final: 0.7214 (tp40) REVERT: D 42 GLN cc_start: 0.8639 (mm110) cc_final: 0.8317 (mm110) REVERT: D 43 ASN cc_start: 0.8476 (t0) cc_final: 0.8253 (t0) REVERT: D 45 THR cc_start: 0.7428 (OUTLIER) cc_final: 0.7102 (t) REVERT: D 54 ASN cc_start: 0.8188 (m110) cc_final: 0.7804 (m110) REVERT: D 117 LEU cc_start: 0.7903 (mp) cc_final: 0.7676 (mt) REVERT: E 147 GLN cc_start: 0.7949 (mt0) cc_final: 0.7639 (mt0) REVERT: E 228 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7378 (tmt170) REVERT: E 238 MET cc_start: 0.8401 (tpp) cc_final: 0.8009 (mmt) REVERT: E 357 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7538 (tp40) REVERT: E 527 LYS cc_start: 0.7712 (tmmt) cc_final: 0.6881 (ttmt) REVERT: E 546 SER cc_start: 0.8563 (t) cc_final: 0.8041 (m) REVERT: E 560 GLN cc_start: 0.7750 (tp40) cc_final: 0.7223 (tp40) REVERT: F 45 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.7087 (t) REVERT: F 54 ASN cc_start: 0.8190 (m110) cc_final: 0.7803 (m110) REVERT: F 117 LEU cc_start: 0.7903 (mp) cc_final: 0.7678 (mt) REVERT: G 147 GLN cc_start: 0.7908 (mt0) cc_final: 0.7625 (mt0) REVERT: G 228 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7382 (tmt170) REVERT: G 238 MET cc_start: 0.8399 (tpp) cc_final: 0.8008 (mmt) REVERT: G 295 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7691 (mt-10) REVERT: G 357 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: G 527 LYS cc_start: 0.7711 (tmmt) cc_final: 0.6882 (ttmt) REVERT: G 546 SER cc_start: 0.8568 (t) cc_final: 0.8046 (m) REVERT: G 560 GLN cc_start: 0.7752 (tp40) cc_final: 0.7224 (tp40) REVERT: H 42 GLN cc_start: 0.8654 (mm110) cc_final: 0.8327 (mm110) REVERT: H 43 ASN cc_start: 0.8525 (t0) cc_final: 0.8289 (t0) REVERT: H 45 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7092 (t) REVERT: H 54 ASN cc_start: 0.8190 (m110) cc_final: 0.7805 (m110) REVERT: H 70 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7772 (mp) REVERT: H 117 LEU cc_start: 0.7906 (mp) cc_final: 0.7684 (mt) outliers start: 32 outliers final: 16 residues processed: 249 average time/residue: 0.3374 time to fit residues: 118.3781 Evaluate side-chains 252 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16152 Z= 0.224 Angle : 0.463 5.660 21824 Z= 0.244 Chirality : 0.039 0.130 2444 Planarity : 0.003 0.025 2752 Dihedral : 3.571 15.679 2164 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.81 % Allowed : 14.10 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1952 helix: 2.04 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.01 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 379 HIS 0.002 0.001 HIS E 258 PHE 0.010 0.001 PHE A 351 TYR 0.013 0.001 TYR G 545 ARG 0.003 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 1.802 Fit side-chains REVERT: A 147 GLN cc_start: 0.7988 (mt0) cc_final: 0.7695 (mt0) REVERT: A 228 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7372 (tmt170) REVERT: A 238 MET cc_start: 0.8490 (tpp) cc_final: 0.8080 (mmt) REVERT: A 357 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: A 527 LYS cc_start: 0.7751 (tmmt) cc_final: 0.6885 (ttmt) REVERT: A 546 SER cc_start: 0.8561 (t) cc_final: 0.7942 (m) REVERT: A 560 GLN cc_start: 0.7767 (tp40) cc_final: 0.7246 (tp40) REVERT: B 23 ASP cc_start: 0.4955 (OUTLIER) cc_final: 0.3946 (p0) REVERT: B 43 ASN cc_start: 0.8450 (t0) cc_final: 0.8208 (t0) REVERT: B 45 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7123 (t) REVERT: B 54 ASN cc_start: 0.8209 (m110) cc_final: 0.7802 (m110) REVERT: B 105 GLU cc_start: 0.7342 (tp30) cc_final: 0.7011 (tt0) REVERT: C 147 GLN cc_start: 0.7974 (mt0) cc_final: 0.7657 (mt0) REVERT: C 228 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7378 (tmt170) REVERT: C 238 MET cc_start: 0.8471 (tpp) cc_final: 0.8079 (mmt) REVERT: C 357 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7542 (tp40) REVERT: C 527 LYS cc_start: 0.7747 (tmmt) cc_final: 0.6883 (ttmt) REVERT: C 546 SER cc_start: 0.8551 (t) cc_final: 0.7932 (m) REVERT: C 560 GLN cc_start: 0.7770 (tp40) cc_final: 0.7251 (tp40) REVERT: D 42 GLN cc_start: 0.8671 (mm110) cc_final: 0.8335 (mm110) REVERT: D 43 ASN cc_start: 0.8473 (t0) cc_final: 0.8148 (t0) REVERT: D 45 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7145 (t) REVERT: D 54 ASN cc_start: 0.8224 (m110) cc_final: 0.7821 (m110) REVERT: E 147 GLN cc_start: 0.7982 (mt0) cc_final: 0.7661 (mt0) REVERT: E 228 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7378 (tmt170) REVERT: E 238 MET cc_start: 0.8470 (tpp) cc_final: 0.8082 (mmt) REVERT: E 357 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7546 (tp40) REVERT: E 527 LYS cc_start: 0.7767 (tmmt) cc_final: 0.6897 (ttmt) REVERT: E 546 SER cc_start: 0.8555 (t) cc_final: 0.7936 (m) REVERT: E 560 GLN cc_start: 0.7776 (tp40) cc_final: 0.7258 (tp40) REVERT: F 43 ASN cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) REVERT: F 45 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7129 (t) REVERT: F 54 ASN cc_start: 0.8199 (m110) cc_final: 0.7792 (m110) REVERT: G 147 GLN cc_start: 0.7966 (mt0) cc_final: 0.7645 (mt0) REVERT: G 228 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7389 (tmt170) REVERT: G 238 MET cc_start: 0.8468 (tpp) cc_final: 0.8079 (mmt) REVERT: G 295 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7683 (mt-10) REVERT: G 357 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: G 527 LYS cc_start: 0.7767 (tmmt) cc_final: 0.6899 (ttmt) REVERT: G 546 SER cc_start: 0.8560 (t) cc_final: 0.7942 (m) REVERT: G 560 GLN cc_start: 0.7774 (tp40) cc_final: 0.7256 (tp40) REVERT: H 42 GLN cc_start: 0.8664 (mm110) cc_final: 0.8325 (mm110) REVERT: H 43 ASN cc_start: 0.8477 (t0) cc_final: 0.8230 (t0) REVERT: H 45 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7136 (t) REVERT: H 54 ASN cc_start: 0.8201 (m110) cc_final: 0.7794 (m110) outliers start: 30 outliers final: 21 residues processed: 255 average time/residue: 0.3331 time to fit residues: 119.8490 Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 125 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN F 108 HIS F 112 ASN G 357 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16152 Z= 0.198 Angle : 0.454 7.400 21824 Z= 0.239 Chirality : 0.038 0.123 2444 Planarity : 0.003 0.023 2752 Dihedral : 3.556 15.809 2164 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.35 % Allowed : 14.10 % Favored : 83.55 % 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: 2.40 (0.19), residues: 1952 helix: 2.06 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.08 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.002 0.001 HIS A 258 PHE 0.012 0.001 PHE G 351 TYR 0.013 0.001 TYR G 545 ARG 0.006 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 1.908 Fit side-chains REVERT: A 147 GLN cc_start: 0.8005 (mt0) cc_final: 0.7670 (mt0) REVERT: A 228 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7398 (tmt170) REVERT: A 238 MET cc_start: 0.8494 (tpp) cc_final: 0.8242 (mmm) REVERT: A 357 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7527 (tp40) REVERT: A 527 LYS cc_start: 0.7772 (tmmt) cc_final: 0.6904 (ttmt) REVERT: A 546 SER cc_start: 0.8556 (t) cc_final: 0.7943 (m) REVERT: A 560 GLN cc_start: 0.7761 (tp40) cc_final: 0.7247 (tp40) REVERT: B 23 ASP cc_start: 0.4960 (OUTLIER) cc_final: 0.3945 (p0) REVERT: B 43 ASN cc_start: 0.8445 (t0) cc_final: 0.8222 (t0) REVERT: B 45 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7100 (t) REVERT: B 54 ASN cc_start: 0.8207 (m110) cc_final: 0.7801 (m110) REVERT: B 105 GLU cc_start: 0.7243 (tp30) cc_final: 0.6890 (tt0) REVERT: C 147 GLN cc_start: 0.8000 (mt0) cc_final: 0.7666 (mt0) REVERT: C 228 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7406 (tmt170) REVERT: C 238 MET cc_start: 0.8478 (tpp) cc_final: 0.8226 (mmm) REVERT: C 357 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7515 (tp40) REVERT: C 527 LYS cc_start: 0.7769 (tmmt) cc_final: 0.6902 (ttmt) REVERT: C 546 SER cc_start: 0.8548 (t) cc_final: 0.7934 (m) REVERT: C 560 GLN cc_start: 0.7762 (tp40) cc_final: 0.7249 (tp40) REVERT: D 42 GLN cc_start: 0.8663 (mm110) cc_final: 0.8301 (mm110) REVERT: D 43 ASN cc_start: 0.8458 (t0) cc_final: 0.8223 (t0) REVERT: D 45 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7108 (t) REVERT: D 54 ASN cc_start: 0.8203 (m110) cc_final: 0.7797 (m110) REVERT: E 147 GLN cc_start: 0.8010 (mt0) cc_final: 0.7672 (mt0) REVERT: E 228 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7401 (tmt170) REVERT: E 238 MET cc_start: 0.8477 (tpp) cc_final: 0.8225 (mmm) REVERT: E 357 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: E 527 LYS cc_start: 0.7760 (tmmt) cc_final: 0.6902 (ttmt) REVERT: E 546 SER cc_start: 0.8550 (t) cc_final: 0.7937 (m) REVERT: E 560 GLN cc_start: 0.7765 (tp40) cc_final: 0.7250 (tp40) REVERT: F 43 ASN cc_start: 0.8431 (t0) cc_final: 0.8202 (t0) REVERT: F 45 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7096 (t) REVERT: F 54 ASN cc_start: 0.8201 (m110) cc_final: 0.7787 (m110) REVERT: G 147 GLN cc_start: 0.7992 (mt0) cc_final: 0.7657 (mt0) REVERT: G 228 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7403 (tmt170) REVERT: G 238 MET cc_start: 0.8478 (tpp) cc_final: 0.8229 (mmm) REVERT: G 295 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7713 (mt-10) REVERT: G 357 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7545 (tp40) REVERT: G 527 LYS cc_start: 0.7760 (tmmt) cc_final: 0.6910 (ttmt) REVERT: G 546 SER cc_start: 0.8556 (t) cc_final: 0.7943 (m) REVERT: G 560 GLN cc_start: 0.7765 (tp40) cc_final: 0.7254 (tp40) REVERT: H 42 GLN cc_start: 0.8657 (mm110) cc_final: 0.8291 (mm110) REVERT: H 43 ASN cc_start: 0.8462 (t0) cc_final: 0.8226 (t0) REVERT: H 45 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7103 (t) REVERT: H 54 ASN cc_start: 0.8202 (m110) cc_final: 0.7789 (m110) outliers start: 39 outliers final: 29 residues processed: 261 average time/residue: 0.3254 time to fit residues: 119.9718 Evaluate side-chains 272 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 125 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN F 112 ASN G 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16152 Z= 0.206 Angle : 0.457 7.659 21824 Z= 0.240 Chirality : 0.038 0.123 2444 Planarity : 0.003 0.022 2752 Dihedral : 3.567 15.696 2164 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.77 % Allowed : 14.22 % Favored : 83.01 % 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: 2.46 (0.19), residues: 1952 helix: 2.11 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.06 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.002 0.001 HIS A 126 PHE 0.011 0.001 PHE G 351 TYR 0.013 0.001 TYR G 545 ARG 0.006 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 1.748 Fit side-chains REVERT: A 147 GLN cc_start: 0.8019 (mt0) cc_final: 0.7794 (mt0) REVERT: A 228 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7394 (tmt170) REVERT: A 238 MET cc_start: 0.8474 (tpp) cc_final: 0.8246 (mmm) REVERT: A 357 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7577 (tp40) REVERT: A 527 LYS cc_start: 0.7780 (tmmt) cc_final: 0.6903 (ttmt) REVERT: A 546 SER cc_start: 0.8560 (t) cc_final: 0.7942 (m) REVERT: A 560 GLN cc_start: 0.7765 (tp40) cc_final: 0.7253 (tp40) REVERT: B 23 ASP cc_start: 0.4982 (OUTLIER) cc_final: 0.3957 (p0) REVERT: B 45 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7165 (t) REVERT: B 54 ASN cc_start: 0.8172 (m110) cc_final: 0.7757 (m110) REVERT: B 105 GLU cc_start: 0.7255 (tp30) cc_final: 0.6894 (tt0) REVERT: C 147 GLN cc_start: 0.8014 (mt0) cc_final: 0.7636 (mt0) REVERT: C 228 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7382 (tmt170) REVERT: C 238 MET cc_start: 0.8458 (tpp) cc_final: 0.8072 (mmt) REVERT: C 357 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: C 527 LYS cc_start: 0.7769 (tmmt) cc_final: 0.6909 (ttmt) REVERT: C 546 SER cc_start: 0.8551 (t) cc_final: 0.7932 (m) REVERT: C 560 GLN cc_start: 0.7760 (tp40) cc_final: 0.7249 (tp40) REVERT: D 42 GLN cc_start: 0.8656 (mm110) cc_final: 0.8323 (mm110) REVERT: D 43 ASN cc_start: 0.8445 (t0) cc_final: 0.8135 (t0) REVERT: D 45 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7150 (t) REVERT: D 54 ASN cc_start: 0.8165 (m110) cc_final: 0.7751 (m110) REVERT: D 144 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8232 (mm-40) REVERT: E 147 GLN cc_start: 0.8023 (mt0) cc_final: 0.7641 (mt0) REVERT: E 228 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7383 (tmt170) REVERT: E 238 MET cc_start: 0.8458 (tpp) cc_final: 0.8073 (mmt) REVERT: E 357 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: E 527 LYS cc_start: 0.7794 (tmmt) cc_final: 0.6916 (ttmt) REVERT: E 546 SER cc_start: 0.8554 (t) cc_final: 0.7934 (m) REVERT: E 560 GLN cc_start: 0.7768 (tp40) cc_final: 0.7256 (tp40) REVERT: F 45 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7174 (t) REVERT: F 54 ASN cc_start: 0.8207 (m110) cc_final: 0.7793 (m110) REVERT: G 147 GLN cc_start: 0.7998 (mt0) cc_final: 0.7627 (mt0) REVERT: G 228 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7382 (tmt170) REVERT: G 238 MET cc_start: 0.8461 (tpp) cc_final: 0.8076 (mmt) REVERT: G 295 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7700 (mt-10) REVERT: G 357 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: G 363 HIS cc_start: 0.7519 (t70) cc_final: 0.7216 (t70) REVERT: G 527 LYS cc_start: 0.7795 (tmmt) cc_final: 0.6913 (ttmt) REVERT: G 546 SER cc_start: 0.8559 (t) cc_final: 0.7940 (m) REVERT: G 560 GLN cc_start: 0.7765 (tp40) cc_final: 0.7256 (tp40) REVERT: H 42 GLN cc_start: 0.8653 (mm110) cc_final: 0.8317 (mm110) REVERT: H 43 ASN cc_start: 0.8448 (t0) cc_final: 0.8134 (t0) REVERT: H 45 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7154 (t) REVERT: H 54 ASN cc_start: 0.8208 (m110) cc_final: 0.7795 (m110) outliers start: 46 outliers final: 33 residues processed: 266 average time/residue: 0.3210 time to fit residues: 120.9925 Evaluate side-chains 278 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 125 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16152 Z= 0.207 Angle : 0.458 7.831 21824 Z= 0.241 Chirality : 0.038 0.124 2444 Planarity : 0.003 0.023 2752 Dihedral : 3.567 15.695 2164 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.59 % Allowed : 14.82 % Favored : 82.59 % 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: 2.49 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.04 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.002 0.001 HIS A 126 PHE 0.010 0.001 PHE G 351 TYR 0.013 0.001 TYR G 545 ARG 0.006 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.982 Fit side-chains REVERT: A 147 GLN cc_start: 0.8073 (mt0) cc_final: 0.7676 (mt0) REVERT: A 228 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7397 (tmt170) REVERT: A 238 MET cc_start: 0.8478 (tpp) cc_final: 0.8216 (mmm) REVERT: A 357 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7554 (tp40) REVERT: A 527 LYS cc_start: 0.7781 (tmmt) cc_final: 0.6901 (ttmt) REVERT: A 546 SER cc_start: 0.8561 (t) cc_final: 0.7942 (m) REVERT: A 560 GLN cc_start: 0.7766 (tp40) cc_final: 0.7255 (tp40) REVERT: B 23 ASP cc_start: 0.4976 (OUTLIER) cc_final: 0.3943 (p0) REVERT: B 43 ASN cc_start: 0.8548 (t0) cc_final: 0.7992 (p0) REVERT: B 45 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7183 (t) REVERT: B 54 ASN cc_start: 0.8196 (m110) cc_final: 0.7781 (m110) REVERT: B 105 GLU cc_start: 0.7274 (tp30) cc_final: 0.6887 (tt0) REVERT: C 147 GLN cc_start: 0.8073 (mt0) cc_final: 0.7674 (mt0) REVERT: C 228 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7359 (tmt170) REVERT: C 238 MET cc_start: 0.8462 (tpp) cc_final: 0.8074 (mmt) REVERT: C 357 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: C 527 LYS cc_start: 0.7774 (tmmt) cc_final: 0.6918 (ttmt) REVERT: C 546 SER cc_start: 0.8553 (t) cc_final: 0.7932 (m) REVERT: C 560 GLN cc_start: 0.7761 (tp40) cc_final: 0.7252 (tp40) REVERT: D 42 GLN cc_start: 0.8671 (mm110) cc_final: 0.8352 (mm110) REVERT: D 43 ASN cc_start: 0.8444 (t0) cc_final: 0.8133 (t0) REVERT: D 45 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7150 (t) REVERT: D 54 ASN cc_start: 0.8188 (m110) cc_final: 0.7772 (m110) REVERT: D 144 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8225 (mm-40) REVERT: E 147 GLN cc_start: 0.8081 (mt0) cc_final: 0.7682 (mt0) REVERT: E 228 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7360 (tmt170) REVERT: E 238 MET cc_start: 0.8463 (tpp) cc_final: 0.8077 (mmt) REVERT: E 357 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7549 (tp40) REVERT: E 527 LYS cc_start: 0.7799 (tmmt) cc_final: 0.6922 (ttmt) REVERT: E 546 SER cc_start: 0.8555 (t) cc_final: 0.7936 (m) REVERT: E 560 GLN cc_start: 0.7769 (tp40) cc_final: 0.7259 (tp40) REVERT: F 45 THR cc_start: 0.7485 (OUTLIER) cc_final: 0.7155 (t) REVERT: F 54 ASN cc_start: 0.8208 (m110) cc_final: 0.7793 (m110) REVERT: G 147 GLN cc_start: 0.8053 (mt0) cc_final: 0.7658 (mt0) REVERT: G 228 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7360 (tmt170) REVERT: G 238 MET cc_start: 0.8486 (tpp) cc_final: 0.8090 (mmt) REVERT: G 357 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7562 (tp40) REVERT: G 363 HIS cc_start: 0.7542 (t70) cc_final: 0.7275 (t70) REVERT: G 527 LYS cc_start: 0.7799 (tmmt) cc_final: 0.6924 (ttmt) REVERT: G 546 SER cc_start: 0.8561 (t) cc_final: 0.7941 (m) REVERT: G 560 GLN cc_start: 0.7764 (tp40) cc_final: 0.7258 (tp40) REVERT: H 42 GLN cc_start: 0.8669 (mm110) cc_final: 0.8347 (mm110) REVERT: H 43 ASN cc_start: 0.8447 (t0) cc_final: 0.8133 (t0) REVERT: H 45 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7162 (t) REVERT: H 54 ASN cc_start: 0.8211 (m110) cc_final: 0.7796 (m110) outliers start: 43 outliers final: 33 residues processed: 268 average time/residue: 0.3349 time to fit residues: 128.6054 Evaluate side-chains 283 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16152 Z= 0.195 Angle : 0.457 8.066 21824 Z= 0.239 Chirality : 0.038 0.122 2444 Planarity : 0.003 0.022 2752 Dihedral : 3.547 15.636 2164 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.59 % Allowed : 14.94 % Favored : 82.47 % 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: 2.56 (0.19), residues: 1952 helix: 2.18 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.00 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.002 0.001 HIS A 126 PHE 0.011 0.001 PHE G 351 TYR 0.012 0.001 TYR G 545 ARG 0.006 0.000 ARG D 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 1.876 Fit side-chains REVERT: A 147 GLN cc_start: 0.8084 (mt0) cc_final: 0.7684 (mt0) REVERT: A 228 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7383 (tmt170) REVERT: A 238 MET cc_start: 0.8470 (tpp) cc_final: 0.8069 (mmt) REVERT: A 357 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7549 (tp40) REVERT: A 527 LYS cc_start: 0.7778 (tmmt) cc_final: 0.6899 (ttmt) REVERT: A 546 SER cc_start: 0.8558 (t) cc_final: 0.7940 (m) REVERT: A 560 GLN cc_start: 0.7762 (tp40) cc_final: 0.7254 (tp40) REVERT: B 23 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.3918 (p0) REVERT: B 42 GLN cc_start: 0.8731 (mm110) cc_final: 0.8180 (mm110) REVERT: B 43 ASN cc_start: 0.8562 (t0) cc_final: 0.8023 (p0) REVERT: B 45 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7165 (t) REVERT: B 54 ASN cc_start: 0.8195 (m110) cc_final: 0.7781 (m110) REVERT: B 105 GLU cc_start: 0.7334 (tp30) cc_final: 0.6957 (tt0) REVERT: C 147 GLN cc_start: 0.8082 (mt0) cc_final: 0.7681 (mt0) REVERT: C 228 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7207 (tmt170) REVERT: C 238 MET cc_start: 0.8460 (tpp) cc_final: 0.8080 (mmt) REVERT: C 357 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: C 527 LYS cc_start: 0.7801 (tmmt) cc_final: 0.6923 (ttmt) REVERT: C 546 SER cc_start: 0.8550 (t) cc_final: 0.7931 (m) REVERT: C 560 GLN cc_start: 0.7757 (tp40) cc_final: 0.7250 (tp40) REVERT: D 42 GLN cc_start: 0.8677 (mm110) cc_final: 0.8366 (mm110) REVERT: D 43 ASN cc_start: 0.8441 (t0) cc_final: 0.8135 (t0) REVERT: D 45 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7147 (t) REVERT: D 54 ASN cc_start: 0.8168 (m110) cc_final: 0.7749 (m110) REVERT: D 144 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8224 (mm-40) REVERT: E 147 GLN cc_start: 0.8091 (mt0) cc_final: 0.7689 (mt0) REVERT: E 228 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7212 (tmt170) REVERT: E 238 MET cc_start: 0.8458 (tpp) cc_final: 0.8080 (mmt) REVERT: E 357 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: E 527 LYS cc_start: 0.7798 (tmmt) cc_final: 0.6921 (ttmt) REVERT: E 546 SER cc_start: 0.8553 (t) cc_final: 0.7934 (m) REVERT: E 560 GLN cc_start: 0.7764 (tp40) cc_final: 0.7257 (tp40) REVERT: F 42 GLN cc_start: 0.8713 (mm110) cc_final: 0.8411 (mm110) REVERT: F 43 ASN cc_start: 0.8561 (t0) cc_final: 0.8016 (p0) REVERT: F 45 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7169 (t) REVERT: F 54 ASN cc_start: 0.8209 (m110) cc_final: 0.7793 (m110) REVERT: G 147 GLN cc_start: 0.8061 (mt0) cc_final: 0.7662 (mt0) REVERT: G 228 ARG cc_start: 0.7825 (mtt180) cc_final: 0.7366 (tmt170) REVERT: G 238 MET cc_start: 0.8468 (tpp) cc_final: 0.8084 (mmt) REVERT: G 357 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (tp40) REVERT: G 363 HIS cc_start: 0.7533 (t70) cc_final: 0.7267 (t70) REVERT: G 527 LYS cc_start: 0.7798 (tmmt) cc_final: 0.6924 (ttmt) REVERT: G 546 SER cc_start: 0.8559 (t) cc_final: 0.7941 (m) REVERT: G 560 GLN cc_start: 0.7765 (tp40) cc_final: 0.7258 (tp40) REVERT: H 42 GLN cc_start: 0.8674 (mm110) cc_final: 0.8360 (mm110) REVERT: H 43 ASN cc_start: 0.8442 (t0) cc_final: 0.8133 (t0) REVERT: H 45 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7164 (t) REVERT: H 54 ASN cc_start: 0.8211 (m110) cc_final: 0.7796 (m110) outliers start: 43 outliers final: 30 residues processed: 267 average time/residue: 0.3297 time to fit residues: 123.8756 Evaluate side-chains 280 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102959 restraints weight = 20751.399| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.81 r_work: 0.3070 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16152 Z= 0.244 Angle : 0.478 7.937 21824 Z= 0.251 Chirality : 0.039 0.131 2444 Planarity : 0.003 0.026 2752 Dihedral : 3.602 16.031 2164 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.47 % Allowed : 14.94 % Favored : 82.59 % 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: 1952 helix: 2.10 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.02 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.002 0.001 HIS A 126 PHE 0.011 0.001 PHE G 351 TYR 0.014 0.001 TYR G 545 ARG 0.006 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.56 seconds wall clock time: 69 minutes 56.60 seconds (4196.60 seconds total)