Starting phenix.real_space_refine on Fri Sep 27 20:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/09_2024/5uvn_8608_neut.cif" } resolution = 3.96 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 10770 2.51 5 N 2886 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16902 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "E" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Chain: "F" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2582 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 162 Chain: "F" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 235 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'TRANS': 46} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'UNK:plan-1': 47} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 10.10, per 1000 atoms: 0.60 Number of scatterers: 16902 At special positions: 0 Unit cell: (106.11, 111.35, 168.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 3228 8.00 N 2886 7.00 C 10770 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 30.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU A 95 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 98 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 436 through 467 Processing helix chain 'B' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU B 95 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 430 Processing helix chain 'B' and resid 436 through 467 Processing helix chain 'C' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU C 95 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 281 Processing helix chain 'C' and resid 322 through 333 removed outlier: 3.630A pdb=" N GLN C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 346 Processing helix chain 'C' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 436 through 467 Processing helix chain 'D' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU D 95 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 98 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 238 through 245 removed outlier: 4.035A pdb=" N THR D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 356 through 365 removed outlier: 4.180A pdb=" N LYS D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 Processing helix chain 'D' and resid 436 through 467 Processing helix chain 'E' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU E 95 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 208 through 212 Processing helix chain 'E' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 281 Processing helix chain 'E' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN E 327 " --> pdb=" O PRO E 323 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 430 Processing helix chain 'E' and resid 436 through 467 Processing helix chain 'F' and resid 92 through 98 removed outlier: 4.086A pdb=" N GLU F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 98 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 238 through 245 removed outlier: 4.036A pdb=" N THR F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 281 Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.631A pdb=" N GLN F 327 " --> pdb=" O PRO F 323 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 356 through 365 removed outlier: 4.181A pdb=" N LYS F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 430 Processing helix chain 'F' and resid 436 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU A 85 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 75 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS A 87 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 62 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE A 104 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE A 178 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 186 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 203 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE A 268 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 161 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 236 Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU A 386 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 306 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 313 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 307 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE A 407 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 289 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU B 85 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 75 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS B 87 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 62 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE B 104 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE B 178 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL B 186 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 203 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE B 268 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 161 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 236 Processing sheet with id=AB2, first strand: chain 'B' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU B 386 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B 306 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 313 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 307 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE B 407 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 289 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU C 85 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA C 75 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS C 87 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 62 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE C 104 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE C 178 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 186 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 203 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE C 268 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 161 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 236 Processing sheet with id=AB7, first strand: chain 'C' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU C 386 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU C 306 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 313 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE C 307 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 407 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 289 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 49 removed outlier: 6.838A pdb=" N GLU D 85 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA D 75 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS D 87 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 62 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE D 104 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE D 178 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL D 186 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE D 203 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE D 268 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 161 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 236 Processing sheet with id=AC3, first strand: chain 'D' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU D 386 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU D 306 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 313 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 307 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE D 407 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 289 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 44 through 49 removed outlier: 6.837A pdb=" N GLU E 85 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA E 75 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 87 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 62 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE E 104 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.372A pdb=" N PHE E 178 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL E 186 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 203 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE E 268 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 161 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 370 through 374 removed outlier: 8.219A pdb=" N LEU E 386 " --> pdb=" O PRO E 304 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU E 306 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 313 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE E 307 " --> pdb=" O ARG E 311 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE E 407 " --> pdb=" O ASP E 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 289 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.839A pdb=" N GLU F 85 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA F 75 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS F 87 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE F 62 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 131 removed outlier: 6.478A pdb=" N PHE F 104 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.371A pdb=" N PHE F 178 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL F 186 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE F 203 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N PHE F 268 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 161 " --> pdb=" O PHE F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 370 through 374 removed outlier: 8.220A pdb=" N LEU F 386 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU F 306 " --> pdb=" O LEU F 386 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY F 313 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE F 307 " --> pdb=" O ARG F 311 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE F 407 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU F 289 " --> pdb=" O ILE F 407 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2034 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: 8.18 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4940 1.33 - 1.45: 2492 1.45 - 1.57: 9704 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 17172 Sorted by residual: bond pdb=" C LEU F 299 " pdb=" N GLN F 300 " ideal model delta sigma weight residual 1.335 1.216 0.119 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU B 299 " pdb=" N GLN B 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.09e+01 bond pdb=" C LEU A 299 " pdb=" N GLN A 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU D 299 " pdb=" N GLN D 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.08e+01 bond pdb=" C LEU E 299 " pdb=" N GLN E 300 " ideal model delta sigma weight residual 1.335 1.217 0.118 3.59e-02 7.76e+02 1.07e+01 ... (remaining 17167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21671 1.85 - 3.70: 1465 3.70 - 5.56: 277 5.56 - 7.41: 69 7.41 - 9.26: 50 Bond angle restraints: 23532 Sorted by residual: angle pdb=" C SER B 239 " pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 117.23 109.03 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" C SER E 239 " pdb=" CA SER E 239 " pdb=" CB SER E 239 " ideal model delta sigma weight residual 117.23 109.04 8.19 1.36e+00 5.41e-01 3.62e+01 angle pdb=" C SER A 239 " pdb=" CA SER A 239 " pdb=" CB SER A 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER D 239 " pdb=" CA SER D 239 " pdb=" CB SER D 239 " ideal model delta sigma weight residual 117.23 109.06 8.17 1.36e+00 5.41e-01 3.61e+01 angle pdb=" C SER F 239 " pdb=" CA SER F 239 " pdb=" CB SER F 239 " ideal model delta sigma weight residual 117.23 109.08 8.15 1.36e+00 5.41e-01 3.60e+01 ... (remaining 23527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.39: 8351 7.39 - 14.79: 1382 14.79 - 22.18: 293 22.18 - 29.58: 60 29.58 - 36.97: 6 Dihedral angle restraints: 10092 sinusoidal: 3018 harmonic: 7074 Sorted by residual: dihedral pdb=" CA ASP E 294 " pdb=" C ASP E 294 " pdb=" N SER E 295 " pdb=" CA SER E 295 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP D 294 " pdb=" C ASP D 294 " pdb=" N SER D 295 " pdb=" CA SER D 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N SER A 295 " pdb=" CA SER A 295 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1891 0.052 - 0.104: 846 0.104 - 0.155: 180 0.155 - 0.207: 20 0.207 - 0.259: 9 Chirality restraints: 2946 Sorted by residual: chirality pdb=" CG LEU D 170 " pdb=" CB LEU D 170 " pdb=" CD1 LEU D 170 " pdb=" CD2 LEU D 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU F 170 " pdb=" CB LEU F 170 " pdb=" CD1 LEU F 170 " pdb=" CD2 LEU F 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2943 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK C 456 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C UNK C 456 " -0.064 2.00e-02 2.50e+03 pdb=" O UNK C 456 " 0.024 2.00e-02 2.50e+03 pdb=" N UNK C 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK E 456 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C UNK E 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK E 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK E 457 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 456 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C UNK D 456 " -0.063 2.00e-02 2.50e+03 pdb=" O UNK D 456 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK D 457 " 0.021 2.00e-02 2.50e+03 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 244 2.59 - 3.17: 16152 3.17 - 3.75: 23691 3.75 - 4.32: 32837 4.32 - 4.90: 53502 Nonbonded interactions: 126426 Sorted by model distance: nonbonded pdb=" NH1 ARG A 65 " pdb=" O LEU F 81 " model vdw 2.013 3.120 nonbonded pdb=" O LEU D 81 " pdb=" NH1 ARG E 65 " model vdw 2.016 3.120 nonbonded pdb=" O LEU A 81 " pdb=" NH1 ARG B 65 " model vdw 2.017 3.120 nonbonded pdb=" O LEU C 81 " pdb=" NH1 ARG D 65 " model vdw 2.023 3.120 nonbonded pdb=" O LEU B 81 " pdb=" NH1 ARG C 65 " model vdw 2.024 3.120 ... (remaining 126421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 43.000 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.012 0.119 17172 Z= 0.798 Angle : 1.132 9.262 23532 Z= 0.594 Chirality : 0.059 0.259 2946 Planarity : 0.008 0.078 3054 Dihedral : 7.901 36.971 5544 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.54 % Favored : 90.91 % Rotamer: Outliers : 0.40 % Allowed : 0.00 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.03 (0.14), residues: 2178 helix: -3.73 (0.20), residues: 354 sheet: -2.16 (0.14), residues: 612 loop : -2.64 (0.14), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP E 219 HIS 0.004 0.001 HIS C 99 PHE 0.032 0.003 PHE F 250 TYR 0.016 0.003 TYR B 181 ARG 0.009 0.002 ARG E 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 422 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8839 (t0) cc_final: 0.8589 (t0) REVERT: A 63 LYS cc_start: 0.8672 (pttt) cc_final: 0.8310 (pttp) REVERT: A 71 VAL cc_start: 0.9024 (t) cc_final: 0.8768 (p) REVERT: A 87 LYS cc_start: 0.7161 (mttt) cc_final: 0.6654 (mttm) REVERT: A 105 TRP cc_start: 0.8495 (p90) cc_final: 0.7306 (p90) REVERT: A 143 ASP cc_start: 0.9040 (p0) cc_final: 0.8820 (p0) REVERT: A 342 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7227 (pt0) REVERT: A 373 LYS cc_start: 0.7229 (mttt) cc_final: 0.6902 (mttm) REVERT: B 51 ASN cc_start: 0.8929 (t0) cc_final: 0.8663 (t0) REVERT: B 63 LYS cc_start: 0.8813 (pttt) cc_final: 0.8150 (pttp) REVERT: B 87 LYS cc_start: 0.7162 (mttt) cc_final: 0.6768 (mttm) REVERT: B 143 ASP cc_start: 0.9066 (p0) cc_final: 0.8803 (p0) REVERT: B 215 ASN cc_start: 0.6255 (m-40) cc_final: 0.6039 (m110) REVERT: B 274 GLN cc_start: 0.7409 (mt0) cc_final: 0.7197 (mt0) REVERT: B 342 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8353 (mt-10) REVERT: B 373 LYS cc_start: 0.7480 (mttt) cc_final: 0.6870 (mttm) REVERT: C 61 THR cc_start: 0.8315 (p) cc_final: 0.8090 (p) REVERT: C 63 LYS cc_start: 0.8518 (pttt) cc_final: 0.8142 (pttp) REVERT: C 71 VAL cc_start: 0.8914 (t) cc_final: 0.8502 (p) REVERT: C 143 ASP cc_start: 0.9095 (p0) cc_final: 0.8782 (p0) REVERT: C 145 LEU cc_start: 0.7938 (mt) cc_final: 0.7658 (mt) REVERT: C 161 ILE cc_start: 0.8579 (mt) cc_final: 0.8334 (mt) REVERT: C 226 VAL cc_start: 0.8931 (t) cc_final: 0.8697 (p) REVERT: C 363 LEU cc_start: 0.9243 (mt) cc_final: 0.8966 (mt) REVERT: C 373 LYS cc_start: 0.7272 (mttt) cc_final: 0.6794 (mttm) REVERT: D 51 ASN cc_start: 0.8854 (t0) cc_final: 0.8612 (t0) REVERT: D 63 LYS cc_start: 0.8671 (pttt) cc_final: 0.8295 (pttp) REVERT: D 71 VAL cc_start: 0.9023 (t) cc_final: 0.8766 (p) REVERT: D 87 LYS cc_start: 0.7157 (mttt) cc_final: 0.6652 (mttm) REVERT: D 105 TRP cc_start: 0.8467 (p90) cc_final: 0.7235 (p90) REVERT: D 143 ASP cc_start: 0.9058 (p0) cc_final: 0.8846 (p0) REVERT: D 342 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7227 (pt0) REVERT: D 373 LYS cc_start: 0.7262 (mttt) cc_final: 0.6926 (mttm) REVERT: E 51 ASN cc_start: 0.8932 (t0) cc_final: 0.8657 (t0) REVERT: E 63 LYS cc_start: 0.8813 (pttt) cc_final: 0.8138 (pttp) REVERT: E 87 LYS cc_start: 0.7164 (mttt) cc_final: 0.6769 (mttm) REVERT: E 143 ASP cc_start: 0.9064 (p0) cc_final: 0.8811 (p0) REVERT: E 215 ASN cc_start: 0.6252 (m-40) cc_final: 0.6032 (m110) REVERT: E 274 GLN cc_start: 0.7398 (mt0) cc_final: 0.7187 (mt0) REVERT: E 342 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8352 (mt-10) REVERT: E 373 LYS cc_start: 0.7451 (mttt) cc_final: 0.6855 (mttm) REVERT: F 61 THR cc_start: 0.8329 (p) cc_final: 0.8103 (p) REVERT: F 63 LYS cc_start: 0.8494 (pttt) cc_final: 0.8153 (pttp) REVERT: F 71 VAL cc_start: 0.8868 (t) cc_final: 0.8473 (p) REVERT: F 143 ASP cc_start: 0.9103 (p0) cc_final: 0.8782 (p0) REVERT: F 145 LEU cc_start: 0.7996 (mt) cc_final: 0.7673 (mt) REVERT: F 161 ILE cc_start: 0.8582 (mt) cc_final: 0.8336 (mt) REVERT: F 226 VAL cc_start: 0.8947 (t) cc_final: 0.8710 (p) REVERT: F 274 GLN cc_start: 0.7193 (mt0) cc_final: 0.6903 (mt0) REVERT: F 363 LEU cc_start: 0.9152 (mt) cc_final: 0.8901 (mt) REVERT: F 373 LYS cc_start: 0.7335 (mttt) cc_final: 0.6898 (mttm) outliers start: 6 outliers final: 0 residues processed: 422 average time/residue: 0.3006 time to fit residues: 189.3035 Evaluate side-chains 269 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 215 ASN A 285 HIS A 359 HIS A 376 ASN B 285 HIS B 359 HIS B 376 ASN C 215 ASN C 285 HIS C 359 HIS C 376 ASN D 201 GLN D 215 ASN D 285 HIS D 359 HIS D 376 ASN E 285 HIS E 359 HIS E 376 ASN F 215 ASN F 285 HIS F 359 HIS F 376 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17172 Z= 0.229 Angle : 0.739 8.438 23532 Z= 0.380 Chirality : 0.048 0.152 2946 Planarity : 0.006 0.063 3054 Dihedral : 6.492 22.727 2592 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.54 % Favored : 90.63 % Rotamer: Outliers : 1.21 % Allowed : 9.04 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.16), residues: 2178 helix: -2.85 (0.20), residues: 396 sheet: -1.53 (0.16), residues: 702 loop : -1.99 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP D 105 HIS 0.005 0.001 HIS C 99 PHE 0.017 0.002 PHE B 292 TYR 0.012 0.001 TYR E 288 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 358 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8529 (pttt) cc_final: 0.8115 (pttp) REVERT: A 87 LYS cc_start: 0.7253 (mttt) cc_final: 0.6578 (mttm) REVERT: A 143 ASP cc_start: 0.9073 (p0) cc_final: 0.8823 (p0) REVERT: A 216 VAL cc_start: 0.8435 (t) cc_final: 0.8104 (t) REVERT: A 342 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7277 (pt0) REVERT: A 373 LYS cc_start: 0.7163 (mttt) cc_final: 0.6669 (mttm) REVERT: B 63 LYS cc_start: 0.8670 (pttt) cc_final: 0.8335 (pttp) REVERT: B 87 LYS cc_start: 0.7297 (mttt) cc_final: 0.6717 (mttm) REVERT: B 143 ASP cc_start: 0.8887 (p0) cc_final: 0.8674 (p0) REVERT: B 216 VAL cc_start: 0.8236 (t) cc_final: 0.7826 (t) REVERT: B 342 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7324 (pt0) REVERT: B 373 LYS cc_start: 0.7423 (mttt) cc_final: 0.6806 (mttm) REVERT: C 63 LYS cc_start: 0.8660 (pttt) cc_final: 0.8300 (pttp) REVERT: C 293 LYS cc_start: 0.6866 (pttp) cc_final: 0.6556 (ptpt) REVERT: C 363 LEU cc_start: 0.8704 (mt) cc_final: 0.8504 (mm) REVERT: C 373 LYS cc_start: 0.7190 (mttt) cc_final: 0.6673 (mttm) REVERT: D 63 LYS cc_start: 0.8521 (pttt) cc_final: 0.8109 (pttp) REVERT: D 87 LYS cc_start: 0.7254 (mttt) cc_final: 0.6578 (mttm) REVERT: D 143 ASP cc_start: 0.9070 (p0) cc_final: 0.8811 (p0) REVERT: D 216 VAL cc_start: 0.8433 (t) cc_final: 0.8097 (t) REVERT: D 342 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7276 (pt0) REVERT: D 373 LYS cc_start: 0.7202 (mttt) cc_final: 0.6659 (mttm) REVERT: E 63 LYS cc_start: 0.8671 (pttt) cc_final: 0.8333 (pttp) REVERT: E 87 LYS cc_start: 0.7290 (mttt) cc_final: 0.6717 (mttm) REVERT: E 143 ASP cc_start: 0.8895 (p0) cc_final: 0.8673 (p0) REVERT: E 216 VAL cc_start: 0.8236 (t) cc_final: 0.7831 (t) REVERT: E 342 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7333 (pt0) REVERT: E 373 LYS cc_start: 0.7391 (mttt) cc_final: 0.6824 (mttm) REVERT: F 63 LYS cc_start: 0.8649 (pttt) cc_final: 0.8302 (pttp) REVERT: F 293 LYS cc_start: 0.6880 (pttp) cc_final: 0.6588 (ptpt) REVERT: F 373 LYS cc_start: 0.7191 (mttt) cc_final: 0.6691 (mttm) outliers start: 18 outliers final: 14 residues processed: 368 average time/residue: 0.2772 time to fit residues: 153.7093 Evaluate side-chains 292 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 278 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17172 Z= 0.253 Angle : 0.707 10.872 23532 Z= 0.360 Chirality : 0.048 0.148 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.891 23.326 2592 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.17 % Favored : 91.00 % Rotamer: Outliers : 3.98 % Allowed : 9.38 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2178 helix: -1.40 (0.24), residues: 360 sheet: -1.03 (0.17), residues: 654 loop : -2.02 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 105 HIS 0.004 0.001 HIS C 99 PHE 0.017 0.002 PHE E 250 TYR 0.009 0.001 TYR E 288 ARG 0.003 0.000 ARG F 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 315 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8537 (pttt) cc_final: 0.8167 (pttp) REVERT: A 87 LYS cc_start: 0.7275 (mttt) cc_final: 0.6593 (mttm) REVERT: A 145 LEU cc_start: 0.7547 (mp) cc_final: 0.7164 (mt) REVERT: A 216 VAL cc_start: 0.8511 (t) cc_final: 0.8120 (t) REVERT: A 342 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7152 (pt0) REVERT: A 373 LYS cc_start: 0.7206 (mttt) cc_final: 0.6615 (mttm) REVERT: B 63 LYS cc_start: 0.8723 (pttt) cc_final: 0.8248 (pttp) REVERT: B 80 ASP cc_start: 0.6348 (p0) cc_final: 0.6135 (p0) REVERT: B 87 LYS cc_start: 0.7259 (mttt) cc_final: 0.6698 (mttm) REVERT: B 143 ASP cc_start: 0.8930 (p0) cc_final: 0.8661 (p0) REVERT: B 216 VAL cc_start: 0.8176 (t) cc_final: 0.7763 (t) REVERT: B 293 LYS cc_start: 0.7092 (pttm) cc_final: 0.6676 (ptmt) REVERT: B 342 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7174 (pt0) REVERT: B 373 LYS cc_start: 0.7492 (mttt) cc_final: 0.6704 (mttm) REVERT: C 63 LYS cc_start: 0.8530 (pttt) cc_final: 0.8263 (pttp) REVERT: C 265 LYS cc_start: 0.7048 (mmtt) cc_final: 0.5970 (tppt) REVERT: C 373 LYS cc_start: 0.7210 (mttt) cc_final: 0.6734 (mttm) REVERT: D 63 LYS cc_start: 0.8532 (pttt) cc_final: 0.8171 (pttp) REVERT: D 87 LYS cc_start: 0.7277 (mttt) cc_final: 0.6596 (mttm) REVERT: D 145 LEU cc_start: 0.7538 (mp) cc_final: 0.7156 (mt) REVERT: D 216 VAL cc_start: 0.8522 (t) cc_final: 0.8121 (t) REVERT: D 342 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7151 (pt0) REVERT: D 373 LYS cc_start: 0.7219 (mttt) cc_final: 0.6617 (mttm) REVERT: E 63 LYS cc_start: 0.8728 (pttt) cc_final: 0.8246 (pttp) REVERT: E 80 ASP cc_start: 0.6355 (p0) cc_final: 0.6137 (p0) REVERT: E 87 LYS cc_start: 0.7251 (mttt) cc_final: 0.6695 (mttm) REVERT: E 143 ASP cc_start: 0.8933 (p0) cc_final: 0.8668 (p0) REVERT: E 216 VAL cc_start: 0.8173 (t) cc_final: 0.7769 (t) REVERT: E 293 LYS cc_start: 0.7116 (pttm) cc_final: 0.6687 (ptmt) REVERT: E 342 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7193 (pt0) REVERT: E 373 LYS cc_start: 0.7506 (mttt) cc_final: 0.6728 (mttm) REVERT: F 63 LYS cc_start: 0.8588 (pttt) cc_final: 0.8291 (pttp) REVERT: F 108 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7484 (tppp) REVERT: F 265 LYS cc_start: 0.7052 (mmtt) cc_final: 0.5972 (tppt) REVERT: F 373 LYS cc_start: 0.7288 (mttt) cc_final: 0.6776 (mttm) outliers start: 59 outliers final: 33 residues processed: 353 average time/residue: 0.2453 time to fit residues: 134.5618 Evaluate side-chains 308 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 274 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN D 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17172 Z= 0.398 Angle : 0.773 8.290 23532 Z= 0.390 Chirality : 0.050 0.179 2946 Planarity : 0.006 0.066 3054 Dihedral : 5.958 21.114 2592 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.23 % Favored : 89.94 % Rotamer: Outliers : 4.25 % Allowed : 12.75 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.54 (0.17), residues: 2178 helix: -0.67 (0.27), residues: 342 sheet: -1.54 (0.16), residues: 762 loop : -2.10 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 219 HIS 0.003 0.001 HIS C 99 PHE 0.021 0.002 PHE A 250 TYR 0.012 0.002 TYR D 288 ARG 0.003 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 275 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8574 (pttt) cc_final: 0.8240 (pttp) REVERT: A 87 LYS cc_start: 0.7253 (mttt) cc_final: 0.6947 (mttm) REVERT: A 342 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7417 (pt0) REVERT: A 373 LYS cc_start: 0.7234 (mttt) cc_final: 0.6617 (mttm) REVERT: B 63 LYS cc_start: 0.8807 (pttt) cc_final: 0.8266 (pttp) REVERT: B 80 ASP cc_start: 0.6594 (p0) cc_final: 0.6283 (p0) REVERT: B 87 LYS cc_start: 0.7289 (mttt) cc_final: 0.6764 (mttm) REVERT: B 108 LYS cc_start: 0.7855 (tppp) cc_final: 0.7648 (tppp) REVERT: B 143 ASP cc_start: 0.8965 (p0) cc_final: 0.8730 (p0) REVERT: B 161 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 216 VAL cc_start: 0.8430 (t) cc_final: 0.8152 (t) REVERT: B 220 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7365 (tttp) REVERT: B 373 LYS cc_start: 0.7513 (mttt) cc_final: 0.6691 (mttm) REVERT: C 63 LYS cc_start: 0.8604 (pttt) cc_final: 0.8313 (pttp) REVERT: C 131 GLN cc_start: 0.7907 (tt0) cc_final: 0.7464 (tt0) REVERT: C 220 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6858 (tttp) REVERT: C 265 LYS cc_start: 0.7225 (mmtt) cc_final: 0.5949 (tppt) REVERT: C 373 LYS cc_start: 0.7406 (mttt) cc_final: 0.6767 (mttm) REVERT: D 63 LYS cc_start: 0.8576 (pttt) cc_final: 0.8250 (pttp) REVERT: D 87 LYS cc_start: 0.7258 (mttt) cc_final: 0.6951 (mttm) REVERT: D 342 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7417 (pt0) REVERT: D 373 LYS cc_start: 0.7256 (mttt) cc_final: 0.6603 (mttm) REVERT: E 63 LYS cc_start: 0.8815 (pttt) cc_final: 0.8266 (pttp) REVERT: E 80 ASP cc_start: 0.6647 (p0) cc_final: 0.6378 (p0) REVERT: E 87 LYS cc_start: 0.7277 (mttt) cc_final: 0.6762 (mttm) REVERT: E 108 LYS cc_start: 0.7858 (tppp) cc_final: 0.7646 (tppp) REVERT: E 143 ASP cc_start: 0.8969 (p0) cc_final: 0.8737 (p0) REVERT: E 161 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8201 (mp) REVERT: E 216 VAL cc_start: 0.8433 (t) cc_final: 0.8158 (t) REVERT: E 220 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7219 (tttp) REVERT: E 373 LYS cc_start: 0.7540 (mttt) cc_final: 0.6699 (mttm) REVERT: F 63 LYS cc_start: 0.8603 (pttt) cc_final: 0.8319 (pttp) REVERT: F 108 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7397 (ttpp) REVERT: F 220 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6801 (tttp) REVERT: F 265 LYS cc_start: 0.7211 (mmtt) cc_final: 0.5938 (tppt) REVERT: F 373 LYS cc_start: 0.7429 (mttt) cc_final: 0.6794 (mttm) outliers start: 63 outliers final: 47 residues processed: 318 average time/residue: 0.2703 time to fit residues: 130.7357 Evaluate side-chains 315 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17172 Z= 0.377 Angle : 0.756 14.766 23532 Z= 0.380 Chirality : 0.049 0.144 2946 Planarity : 0.006 0.068 3054 Dihedral : 5.828 23.795 2592 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.37 % Favored : 89.81 % Rotamer: Outliers : 4.52 % Allowed : 14.04 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.61 (0.17), residues: 2178 helix: -0.57 (0.27), residues: 360 sheet: -1.57 (0.16), residues: 774 loop : -2.24 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 219 HIS 0.002 0.001 HIS A 359 PHE 0.017 0.002 PHE B 250 TYR 0.012 0.002 TYR D 208 ARG 0.003 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8626 (pttt) cc_final: 0.8253 (pttp) REVERT: A 215 ASN cc_start: 0.6352 (m-40) cc_final: 0.6052 (m-40) REVERT: A 342 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7560 (pt0) REVERT: A 363 LEU cc_start: 0.8789 (mt) cc_final: 0.8532 (mp) REVERT: A 373 LYS cc_start: 0.7305 (mttt) cc_final: 0.6708 (mttm) REVERT: B 63 LYS cc_start: 0.8797 (pttt) cc_final: 0.8351 (pttp) REVERT: B 80 ASP cc_start: 0.6873 (p0) cc_final: 0.6619 (p0) REVERT: B 87 LYS cc_start: 0.7334 (mttt) cc_final: 0.6851 (mttm) REVERT: B 143 ASP cc_start: 0.8950 (p0) cc_final: 0.8715 (p0) REVERT: B 161 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 187 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6389 (mt-10) REVERT: B 198 ILE cc_start: 0.8976 (mt) cc_final: 0.8728 (mp) REVERT: B 216 VAL cc_start: 0.8477 (t) cc_final: 0.8244 (t) REVERT: B 220 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7314 (tttp) REVERT: B 373 LYS cc_start: 0.7557 (mttt) cc_final: 0.6680 (mttm) REVERT: C 63 LYS cc_start: 0.8664 (pttt) cc_final: 0.8405 (pttp) REVERT: C 220 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6549 (tttp) REVERT: C 265 LYS cc_start: 0.7173 (mmtt) cc_final: 0.5953 (tppt) REVERT: C 373 LYS cc_start: 0.7310 (mttt) cc_final: 0.6780 (mttm) REVERT: D 63 LYS cc_start: 0.8633 (pttt) cc_final: 0.8260 (pttp) REVERT: D 215 ASN cc_start: 0.6332 (m-40) cc_final: 0.6048 (m-40) REVERT: D 293 LYS cc_start: 0.6901 (ptpt) cc_final: 0.6485 (ptpp) REVERT: D 342 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7568 (pt0) REVERT: D 363 LEU cc_start: 0.8780 (mt) cc_final: 0.8536 (mp) REVERT: D 373 LYS cc_start: 0.7315 (mttt) cc_final: 0.6708 (mttm) REVERT: E 63 LYS cc_start: 0.8808 (pttt) cc_final: 0.8346 (pttp) REVERT: E 80 ASP cc_start: 0.6877 (p0) cc_final: 0.6621 (p0) REVERT: E 87 LYS cc_start: 0.7332 (mttt) cc_final: 0.6856 (mttm) REVERT: E 143 ASP cc_start: 0.8951 (p0) cc_final: 0.8728 (p0) REVERT: E 161 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8112 (mp) REVERT: E 187 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: E 198 ILE cc_start: 0.8982 (mt) cc_final: 0.8728 (mp) REVERT: E 216 VAL cc_start: 0.8479 (t) cc_final: 0.8237 (t) REVERT: E 220 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7079 (tttp) REVERT: E 373 LYS cc_start: 0.7575 (mttt) cc_final: 0.6693 (mttm) REVERT: F 63 LYS cc_start: 0.8635 (pttt) cc_final: 0.8380 (pttp) REVERT: F 108 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7483 (ttpp) REVERT: F 220 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6730 (tttp) REVERT: F 265 LYS cc_start: 0.7169 (mmtt) cc_final: 0.5954 (tppt) REVERT: F 373 LYS cc_start: 0.7341 (mttt) cc_final: 0.6797 (mttm) outliers start: 67 outliers final: 47 residues processed: 327 average time/residue: 0.2630 time to fit residues: 131.2122 Evaluate side-chains 321 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 406 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17172 Z= 0.193 Angle : 0.682 14.715 23532 Z= 0.339 Chirality : 0.046 0.139 2946 Planarity : 0.005 0.064 3054 Dihedral : 5.296 24.246 2592 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.09 % Favored : 90.08 % Rotamer: Outliers : 2.70 % Allowed : 16.60 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.86 (0.17), residues: 2178 helix: 0.24 (0.29), residues: 360 sheet: -0.90 (0.18), residues: 714 loop : -1.98 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 105 HIS 0.001 0.000 HIS F 99 PHE 0.011 0.001 PHE D 292 TYR 0.013 0.001 TYR D 208 ARG 0.003 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 298 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8540 (pttt) cc_final: 0.8213 (pttp) REVERT: A 215 ASN cc_start: 0.6160 (m-40) cc_final: 0.5841 (m-40) REVERT: A 265 LYS cc_start: 0.6880 (mmmt) cc_final: 0.5947 (tppt) REVERT: A 342 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7175 (pt0) REVERT: A 363 LEU cc_start: 0.8803 (mt) cc_final: 0.8557 (mp) REVERT: A 373 LYS cc_start: 0.7194 (mttt) cc_final: 0.6826 (mttm) REVERT: B 63 LYS cc_start: 0.8672 (pttt) cc_final: 0.8408 (pttp) REVERT: B 80 ASP cc_start: 0.6816 (p0) cc_final: 0.6593 (p0) REVERT: B 87 LYS cc_start: 0.7280 (mttt) cc_final: 0.6830 (mttm) REVERT: B 161 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 198 ILE cc_start: 0.8943 (mt) cc_final: 0.8706 (mp) REVERT: B 216 VAL cc_start: 0.8166 (t) cc_final: 0.7803 (t) REVERT: B 220 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6881 (tttp) REVERT: B 265 LYS cc_start: 0.7154 (mmmm) cc_final: 0.6111 (tppt) REVERT: B 373 LYS cc_start: 0.7593 (mttt) cc_final: 0.6731 (mttm) REVERT: C 143 ASP cc_start: 0.8979 (p0) cc_final: 0.8758 (p0) REVERT: C 220 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6300 (tttp) REVERT: C 265 LYS cc_start: 0.6968 (mmtt) cc_final: 0.5890 (tppt) REVERT: C 373 LYS cc_start: 0.7235 (mttt) cc_final: 0.6697 (mttm) REVERT: D 63 LYS cc_start: 0.8552 (pttt) cc_final: 0.8228 (pttp) REVERT: D 215 ASN cc_start: 0.6155 (m-40) cc_final: 0.5854 (m-40) REVERT: D 293 LYS cc_start: 0.6726 (ptpt) cc_final: 0.6524 (ptpp) REVERT: D 342 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7198 (pt0) REVERT: D 373 LYS cc_start: 0.7212 (mttt) cc_final: 0.6829 (mttm) REVERT: E 63 LYS cc_start: 0.8679 (pttt) cc_final: 0.8412 (pttp) REVERT: E 80 ASP cc_start: 0.6837 (p0) cc_final: 0.6627 (p0) REVERT: E 87 LYS cc_start: 0.7273 (mttt) cc_final: 0.6827 (mttm) REVERT: E 161 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.7805 (mp) REVERT: E 198 ILE cc_start: 0.8947 (mt) cc_final: 0.8701 (mp) REVERT: E 216 VAL cc_start: 0.8164 (t) cc_final: 0.7791 (t) REVERT: E 220 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6884 (tttp) REVERT: E 265 LYS cc_start: 0.7156 (mmmm) cc_final: 0.6106 (tppt) REVERT: E 373 LYS cc_start: 0.7599 (mttt) cc_final: 0.6710 (mttm) REVERT: F 108 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7253 (ttpp) REVERT: F 143 ASP cc_start: 0.8994 (p0) cc_final: 0.8777 (p0) REVERT: F 220 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6310 (tttp) REVERT: F 265 LYS cc_start: 0.6945 (mmtt) cc_final: 0.5884 (tppt) REVERT: F 373 LYS cc_start: 0.7215 (mttt) cc_final: 0.6701 (mttm) outliers start: 40 outliers final: 17 residues processed: 330 average time/residue: 0.2620 time to fit residues: 132.8166 Evaluate side-chains 293 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 269 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17172 Z= 0.435 Angle : 0.791 13.167 23532 Z= 0.395 Chirality : 0.049 0.143 2946 Planarity : 0.006 0.067 3054 Dihedral : 5.689 23.284 2592 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.01 % Favored : 89.16 % Rotamer: Outliers : 3.98 % Allowed : 16.94 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.21 (0.17), residues: 2178 helix: 0.02 (0.28), residues: 360 sheet: -1.26 (0.17), residues: 786 loop : -2.15 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP F 219 HIS 0.002 0.001 HIS D 99 PHE 0.021 0.002 PHE E 250 TYR 0.013 0.002 TYR A 181 ARG 0.004 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 270 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8642 (pttt) cc_final: 0.8294 (pttp) REVERT: A 215 ASN cc_start: 0.6233 (m-40) cc_final: 0.5978 (m-40) REVERT: A 342 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7399 (pt0) REVERT: A 373 LYS cc_start: 0.7222 (mttt) cc_final: 0.6874 (mttm) REVERT: B 63 LYS cc_start: 0.8748 (pttt) cc_final: 0.8270 (pttp) REVERT: B 80 ASP cc_start: 0.6991 (p0) cc_final: 0.6765 (p0) REVERT: B 87 LYS cc_start: 0.7340 (mttt) cc_final: 0.6904 (mttm) REVERT: B 161 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 198 ILE cc_start: 0.9016 (mt) cc_final: 0.8772 (mp) REVERT: B 216 VAL cc_start: 0.8519 (t) cc_final: 0.8247 (t) REVERT: B 220 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7102 (tttp) REVERT: B 265 LYS cc_start: 0.7483 (mmmm) cc_final: 0.6408 (tppt) REVERT: B 373 LYS cc_start: 0.7572 (mttt) cc_final: 0.6707 (mttm) REVERT: C 143 ASP cc_start: 0.9096 (p0) cc_final: 0.8877 (p0) REVERT: C 220 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6580 (tttp) REVERT: C 265 LYS cc_start: 0.7128 (mmtt) cc_final: 0.5973 (tppt) REVERT: C 373 LYS cc_start: 0.7271 (mttt) cc_final: 0.6757 (mttm) REVERT: D 63 LYS cc_start: 0.8656 (pttt) cc_final: 0.8295 (pttp) REVERT: D 215 ASN cc_start: 0.6227 (m-40) cc_final: 0.5966 (m-40) REVERT: D 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7411 (pt0) REVERT: D 373 LYS cc_start: 0.7264 (mttt) cc_final: 0.6877 (mttm) REVERT: E 63 LYS cc_start: 0.8748 (pttt) cc_final: 0.8266 (pttp) REVERT: E 80 ASP cc_start: 0.6992 (p0) cc_final: 0.6751 (p0) REVERT: E 87 LYS cc_start: 0.7337 (mttt) cc_final: 0.6905 (mttm) REVERT: E 161 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8045 (mp) REVERT: E 198 ILE cc_start: 0.9015 (mt) cc_final: 0.8765 (mp) REVERT: E 216 VAL cc_start: 0.8513 (t) cc_final: 0.8237 (t) REVERT: E 220 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7159 (tttp) REVERT: E 265 LYS cc_start: 0.7486 (mmmm) cc_final: 0.6408 (tppt) REVERT: E 373 LYS cc_start: 0.7521 (mttt) cc_final: 0.6639 (mttm) REVERT: F 108 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7324 (ttpp) REVERT: F 143 ASP cc_start: 0.9041 (p0) cc_final: 0.8821 (p0) REVERT: F 220 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6556 (tttp) REVERT: F 265 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6025 (tppt) REVERT: F 373 LYS cc_start: 0.7274 (mttt) cc_final: 0.6609 (mttm) outliers start: 59 outliers final: 41 residues processed: 313 average time/residue: 0.2674 time to fit residues: 127.8322 Evaluate side-chains 314 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 266 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 157 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17172 Z= 0.197 Angle : 0.695 18.572 23532 Z= 0.345 Chirality : 0.047 0.141 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.172 23.949 2592 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.95 % Favored : 90.22 % Rotamer: Outliers : 3.17 % Allowed : 18.56 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.74 (0.18), residues: 2178 helix: 0.55 (0.30), residues: 360 sheet: -0.85 (0.18), residues: 726 loop : -1.97 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 105 HIS 0.001 0.000 HIS D 359 PHE 0.010 0.001 PHE D 292 TYR 0.014 0.001 TYR D 208 ARG 0.004 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8541 (pttt) cc_final: 0.8266 (pttp) REVERT: A 215 ASN cc_start: 0.6053 (m-40) cc_final: 0.5719 (m-40) REVERT: A 265 LYS cc_start: 0.6880 (mmmt) cc_final: 0.5925 (tppt) REVERT: A 342 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7236 (pt0) REVERT: A 373 LYS cc_start: 0.7205 (mttt) cc_final: 0.6787 (mttm) REVERT: B 63 LYS cc_start: 0.8664 (pttt) cc_final: 0.8295 (pttp) REVERT: B 80 ASP cc_start: 0.6893 (p0) cc_final: 0.6665 (p0) REVERT: B 87 LYS cc_start: 0.7316 (mttt) cc_final: 0.6859 (mttm) REVERT: B 161 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8157 (mp) REVERT: B 216 VAL cc_start: 0.8144 (t) cc_final: 0.7756 (t) REVERT: B 220 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6856 (tttp) REVERT: B 265 LYS cc_start: 0.7276 (mmmm) cc_final: 0.7021 (mptt) REVERT: B 373 LYS cc_start: 0.7615 (mttt) cc_final: 0.6761 (mttm) REVERT: C 143 ASP cc_start: 0.9026 (p0) cc_final: 0.8807 (p0) REVERT: C 220 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6278 (tttp) REVERT: C 265 LYS cc_start: 0.6976 (mmtt) cc_final: 0.5895 (tppt) REVERT: C 373 LYS cc_start: 0.7311 (mttt) cc_final: 0.6753 (mttm) REVERT: D 63 LYS cc_start: 0.8557 (pttt) cc_final: 0.8274 (pttp) REVERT: D 215 ASN cc_start: 0.6037 (m-40) cc_final: 0.5727 (m-40) REVERT: D 342 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7255 (pt0) REVERT: D 363 LEU cc_start: 0.8774 (mt) cc_final: 0.8475 (mp) REVERT: D 373 LYS cc_start: 0.7210 (mttt) cc_final: 0.6772 (mttm) REVERT: E 63 LYS cc_start: 0.8669 (pttt) cc_final: 0.8295 (pttp) REVERT: E 80 ASP cc_start: 0.6898 (p0) cc_final: 0.6674 (p0) REVERT: E 87 LYS cc_start: 0.7312 (mttt) cc_final: 0.6858 (mttm) REVERT: E 161 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8156 (mp) REVERT: E 216 VAL cc_start: 0.8130 (t) cc_final: 0.7746 (t) REVERT: E 220 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6863 (tttp) REVERT: E 265 LYS cc_start: 0.7283 (mmmm) cc_final: 0.7023 (mptt) REVERT: E 373 LYS cc_start: 0.7725 (mttt) cc_final: 0.6880 (mttm) REVERT: F 108 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7206 (ttpp) REVERT: F 143 ASP cc_start: 0.9007 (p0) cc_final: 0.8798 (p0) REVERT: F 220 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6224 (tttp) REVERT: F 265 LYS cc_start: 0.6953 (mmtt) cc_final: 0.5889 (tppt) REVERT: F 373 LYS cc_start: 0.7405 (mttt) cc_final: 0.6878 (mttm) outliers start: 47 outliers final: 25 residues processed: 328 average time/residue: 0.2663 time to fit residues: 132.3480 Evaluate side-chains 301 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 269 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 218 PHE Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 0.2980 chunk 169 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17172 Z= 0.254 Angle : 0.723 17.833 23532 Z= 0.356 Chirality : 0.047 0.147 2946 Planarity : 0.005 0.065 3054 Dihedral : 5.138 23.776 2592 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.92 % Favored : 89.07 % Rotamer: Outliers : 3.17 % Allowed : 18.76 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.73 (0.18), residues: 2178 helix: 0.48 (0.30), residues: 360 sheet: -0.81 (0.18), residues: 726 loop : -1.96 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 219 HIS 0.002 0.000 HIS F 99 PHE 0.012 0.001 PHE B 250 TYR 0.018 0.001 TYR D 181 ARG 0.004 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 276 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8565 (pttt) cc_final: 0.8137 (pttp) REVERT: A 215 ASN cc_start: 0.6158 (m-40) cc_final: 0.5878 (m-40) REVERT: A 342 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7310 (pt0) REVERT: A 373 LYS cc_start: 0.7267 (mttt) cc_final: 0.6809 (mttm) REVERT: B 63 LYS cc_start: 0.8637 (pttt) cc_final: 0.8224 (pttp) REVERT: B 80 ASP cc_start: 0.6948 (p0) cc_final: 0.6706 (p0) REVERT: B 87 LYS cc_start: 0.7304 (mttt) cc_final: 0.6852 (mttm) REVERT: B 216 VAL cc_start: 0.8214 (t) cc_final: 0.7813 (t) REVERT: B 220 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6963 (tttp) REVERT: B 373 LYS cc_start: 0.7619 (mttt) cc_final: 0.6773 (mttm) REVERT: C 143 ASP cc_start: 0.9044 (p0) cc_final: 0.8825 (p0) REVERT: C 220 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6412 (tttp) REVERT: C 265 LYS cc_start: 0.6707 (mmtt) cc_final: 0.6159 (tppt) REVERT: C 373 LYS cc_start: 0.7294 (mttt) cc_final: 0.6644 (mttm) REVERT: D 63 LYS cc_start: 0.8563 (pttt) cc_final: 0.8152 (pttp) REVERT: D 160 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8905 (m) REVERT: D 215 ASN cc_start: 0.6174 (m-40) cc_final: 0.5909 (m-40) REVERT: D 265 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6519 (tppt) REVERT: D 342 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7306 (pt0) REVERT: D 363 LEU cc_start: 0.8835 (mt) cc_final: 0.8569 (mp) REVERT: D 373 LYS cc_start: 0.7301 (mttt) cc_final: 0.6776 (mttm) REVERT: E 63 LYS cc_start: 0.8639 (pttt) cc_final: 0.8228 (pttp) REVERT: E 80 ASP cc_start: 0.7046 (p0) cc_final: 0.6819 (p0) REVERT: E 87 LYS cc_start: 0.7311 (mttt) cc_final: 0.6850 (mttm) REVERT: E 216 VAL cc_start: 0.8226 (t) cc_final: 0.7839 (t) REVERT: E 220 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6941 (tttp) REVERT: E 373 LYS cc_start: 0.7583 (mttt) cc_final: 0.6766 (mttm) REVERT: F 108 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7130 (ttpp) REVERT: F 143 ASP cc_start: 0.9022 (p0) cc_final: 0.8796 (p0) REVERT: F 220 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6339 (tttp) REVERT: F 265 LYS cc_start: 0.6762 (mmtt) cc_final: 0.6137 (tppt) REVERT: F 373 LYS cc_start: 0.7235 (mttt) cc_final: 0.6536 (mttm) outliers start: 47 outliers final: 32 residues processed: 314 average time/residue: 0.2655 time to fit residues: 127.3845 Evaluate side-chains 301 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 9.9990 chunk 227 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 220 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 40.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 17172 Z= 0.555 Angle : 0.890 17.015 23532 Z= 0.442 Chirality : 0.052 0.149 2946 Planarity : 0.006 0.071 3054 Dihedral : 5.876 23.431 2592 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.47 % Favored : 88.71 % Rotamer: Outliers : 3.31 % Allowed : 17.88 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.43 (0.17), residues: 2178 helix: -0.10 (0.28), residues: 360 sheet: -1.50 (0.17), residues: 774 loop : -2.22 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP F 219 HIS 0.002 0.001 HIS F 99 PHE 0.026 0.002 PHE B 250 TYR 0.022 0.002 TYR D 181 ARG 0.004 0.001 ARG E 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 247 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8671 (pttt) cc_final: 0.8314 (pttp) REVERT: A 265 LYS cc_start: 0.7161 (mmmt) cc_final: 0.6306 (tppt) REVERT: A 342 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7410 (pt0) REVERT: A 373 LYS cc_start: 0.7250 (mttt) cc_final: 0.6745 (mttp) REVERT: B 63 LYS cc_start: 0.8762 (pttt) cc_final: 0.8218 (pttp) REVERT: B 80 ASP cc_start: 0.7105 (p0) cc_final: 0.6833 (p0) REVERT: B 87 LYS cc_start: 0.7282 (mttt) cc_final: 0.6975 (mmtm) REVERT: B 220 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7305 (tttp) REVERT: B 373 LYS cc_start: 0.7542 (mttt) cc_final: 0.6662 (mttm) REVERT: C 143 ASP cc_start: 0.9064 (p0) cc_final: 0.8843 (p0) REVERT: C 220 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6899 (tttp) REVERT: C 265 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6174 (tppt) REVERT: C 373 LYS cc_start: 0.7452 (mttt) cc_final: 0.6735 (mttm) REVERT: D 63 LYS cc_start: 0.8660 (pttt) cc_final: 0.8301 (pttp) REVERT: D 160 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8826 (m) REVERT: D 265 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6663 (tppt) REVERT: D 342 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7411 (pt0) REVERT: D 363 LEU cc_start: 0.8896 (mt) cc_final: 0.8622 (mp) REVERT: D 373 LYS cc_start: 0.7295 (mttt) cc_final: 0.6779 (mttp) REVERT: E 63 LYS cc_start: 0.8763 (pttt) cc_final: 0.8219 (pttp) REVERT: E 80 ASP cc_start: 0.7105 (p0) cc_final: 0.6830 (p0) REVERT: E 87 LYS cc_start: 0.7286 (mttt) cc_final: 0.6982 (mmtm) REVERT: E 220 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7201 (tttp) REVERT: E 373 LYS cc_start: 0.7517 (mttt) cc_final: 0.6669 (mttm) REVERT: F 108 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7432 (ttpp) REVERT: F 143 ASP cc_start: 0.9043 (p0) cc_final: 0.8807 (p0) REVERT: F 220 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6862 (tttp) REVERT: F 265 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6157 (tppt) REVERT: F 373 LYS cc_start: 0.7411 (mttt) cc_final: 0.6744 (mttm) outliers start: 49 outliers final: 32 residues processed: 283 average time/residue: 0.2827 time to fit residues: 121.7064 Evaluate side-chains 279 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 241 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN F 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099516 restraints weight = 30381.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101433 restraints weight = 21527.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102691 restraints weight = 16942.168| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17172 Z= 0.334 Angle : 0.776 17.025 23532 Z= 0.383 Chirality : 0.048 0.142 2946 Planarity : 0.006 0.068 3054 Dihedral : 5.502 23.218 2592 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.19 % Favored : 89.03 % Rotamer: Outliers : 2.83 % Allowed : 18.89 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.11 (0.18), residues: 2178 helix: 0.14 (0.29), residues: 360 sheet: -1.18 (0.17), residues: 726 loop : -2.09 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 105 HIS 0.001 0.001 HIS A 285 PHE 0.013 0.002 PHE E 250 TYR 0.018 0.002 TYR D 271 ARG 0.004 0.001 ARG E 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.88 seconds wall clock time: 57 minutes 51.11 seconds (3471.11 seconds total)