Starting phenix.real_space_refine on Sun Mar 17 06:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/03_2024/5uvn_8608_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/03_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_8608/03_2024/5uvn_8608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/03_2024/5uvn_8608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/03_2024/5uvn_8608_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uvn_8608/03_2024/5uvn_8608_neut.pdb" } 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 Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16902 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "C" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "D" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "E" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Chain: "F" Number of atoms: 2817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 2817 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 395} Chain breaks: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 10, 'UNK:plan-1': 47, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 209 Time building chain proxies: 9.64, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 3.0 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: 2.26 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: 5.59 Time building geometry restraints manager: 7.03 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: 96.30 - 104.27: 365 104.27 - 112.24: 9447 112.24 - 120.21: 6236 120.21 - 128.18: 7383 128.18 - 136.16: 101 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 2.520 nonbonded pdb=" O LEU D 81 " pdb=" NH1 ARG E 65 " model vdw 2.016 2.520 nonbonded pdb=" O LEU A 81 " pdb=" NH1 ARG B 65 " model vdw 2.017 2.520 nonbonded pdb=" O LEU C 81 " pdb=" NH1 ARG D 65 " model vdw 2.023 2.520 nonbonded pdb=" O LEU B 81 " pdb=" NH1 ARG C 65 " model vdw 2.024 2.520 ... (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 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.690 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 46.160 Find NCS groups from input model: 1.290 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- 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 : 1.797 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: 0.2866 time to fit residues: 178.7141 Evaluate side-chains 269 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 201 GLN 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 201 GLN E 285 HIS E 359 HIS E 376 ASN F 201 GLN F 215 ASN F 285 HIS F 359 HIS F 376 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17172 Z= 0.217 Angle : 0.712 8.032 23532 Z= 0.368 Chirality : 0.047 0.150 2946 Planarity : 0.006 0.063 3054 Dihedral : 6.476 23.379 2592 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.54 % Favored : 90.63 % Rotamer: Outliers : 1.48 % Allowed : 8.43 % Favored : 90.08 % 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: -3.11 (0.16), residues: 2178 helix: -2.82 (0.20), residues: 396 sheet: -1.53 (0.15), residues: 726 loop : -2.06 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 105 HIS 0.005 0.001 HIS C 99 PHE 0.017 0.002 PHE E 292 TYR 0.011 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 384 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 362 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8486 (pttt) cc_final: 0.8104 (pttp) REVERT: A 87 LYS cc_start: 0.7260 (mttt) cc_final: 0.6570 (mttm) REVERT: A 143 ASP cc_start: 0.9005 (p0) cc_final: 0.8681 (p0) REVERT: A 216 VAL cc_start: 0.8440 (t) cc_final: 0.8062 (t) REVERT: A 342 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7236 (pt0) REVERT: A 373 LYS cc_start: 0.7153 (mttt) cc_final: 0.6633 (mttm) REVERT: B 63 LYS cc_start: 0.8684 (pttt) cc_final: 0.8386 (pttp) REVERT: B 87 LYS cc_start: 0.7298 (mttt) cc_final: 0.6711 (mttm) REVERT: B 143 ASP cc_start: 0.8692 (p0) cc_final: 0.8471 (p0) REVERT: B 216 VAL cc_start: 0.8171 (t) cc_final: 0.7766 (t) REVERT: B 342 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7367 (pt0) REVERT: B 373 LYS cc_start: 0.7364 (mttt) cc_final: 0.6763 (mttm) REVERT: C 63 LYS cc_start: 0.8627 (pttt) cc_final: 0.8324 (pttp) REVERT: C 293 LYS cc_start: 0.6915 (pttp) cc_final: 0.6578 (ptpt) REVERT: C 363 LEU cc_start: 0.8722 (mt) cc_final: 0.8520 (mm) REVERT: C 373 LYS cc_start: 0.7201 (mttt) cc_final: 0.6682 (mttm) REVERT: D 63 LYS cc_start: 0.8481 (pttt) cc_final: 0.8108 (pttp) REVERT: D 87 LYS cc_start: 0.7257 (mttt) cc_final: 0.6556 (mttm) REVERT: D 143 ASP cc_start: 0.8998 (p0) cc_final: 0.8684 (p0) REVERT: D 216 VAL cc_start: 0.8439 (t) cc_final: 0.8068 (t) REVERT: D 342 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7236 (pt0) REVERT: D 373 LYS cc_start: 0.7196 (mttt) cc_final: 0.6702 (mttm) REVERT: E 63 LYS cc_start: 0.8659 (pttt) cc_final: 0.8341 (pttp) REVERT: E 87 LYS cc_start: 0.7293 (mttt) cc_final: 0.6700 (mttm) REVERT: E 143 ASP cc_start: 0.8700 (p0) cc_final: 0.8480 (p0) REVERT: E 216 VAL cc_start: 0.8171 (t) cc_final: 0.7763 (t) REVERT: E 342 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7357 (pt0) REVERT: E 373 LYS cc_start: 0.7340 (mttt) cc_final: 0.6753 (mttm) REVERT: F 63 LYS cc_start: 0.8615 (pttt) cc_final: 0.8325 (pttp) REVERT: F 143 ASP cc_start: 0.8880 (p0) cc_final: 0.8668 (p0) REVERT: F 161 ILE cc_start: 0.8315 (mt) cc_final: 0.8028 (mm) REVERT: F 265 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6119 (tppt) REVERT: F 293 LYS cc_start: 0.6927 (pttp) cc_final: 0.6603 (ptpt) REVERT: F 363 LEU cc_start: 0.8743 (mt) cc_final: 0.8521 (mm) REVERT: F 373 LYS cc_start: 0.7229 (mttt) cc_final: 0.6712 (mttm) outliers start: 22 outliers final: 16 residues processed: 374 average time/residue: 0.2706 time to fit residues: 152.8099 Evaluate side-chains 306 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 290 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 61 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 213 THR 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 61 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 230 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 241 optimal weight: 30.0000 chunk 199 optimal weight: 20.0000 chunk 221 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN E 201 GLN F 201 GLN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17172 Z= 0.272 Angle : 0.705 11.573 23532 Z= 0.356 Chirality : 0.047 0.147 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.918 23.578 2592 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.45 % Favored : 90.73 % Rotamer: Outliers : 3.91 % Allowed : 10.46 % Favored : 85.63 % 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: -2.59 (0.16), residues: 2178 helix: -1.50 (0.24), residues: 360 sheet: -1.21 (0.16), residues: 714 loop : -2.12 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 105 HIS 0.003 0.001 HIS D 359 PHE 0.016 0.002 PHE E 250 TYR 0.007 0.001 TYR E 288 ARG 0.003 0.001 ARG C 297 *********************** 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 362 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 304 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8504 (pttt) cc_final: 0.8182 (pttp) REVERT: A 87 LYS cc_start: 0.7291 (mttt) cc_final: 0.6592 (mttm) REVERT: A 145 LEU cc_start: 0.7609 (mp) cc_final: 0.7188 (mt) REVERT: A 161 ILE cc_start: 0.8303 (mt) cc_final: 0.8089 (mm) REVERT: A 216 VAL cc_start: 0.8554 (t) cc_final: 0.8168 (t) REVERT: A 342 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7243 (pt0) REVERT: A 373 LYS cc_start: 0.7165 (mttt) cc_final: 0.6561 (mttm) REVERT: B 63 LYS cc_start: 0.8730 (pttt) cc_final: 0.8255 (pttp) REVERT: B 87 LYS cc_start: 0.7280 (mttt) cc_final: 0.6702 (mttm) REVERT: B 143 ASP cc_start: 0.8649 (p0) cc_final: 0.8449 (p0) REVERT: B 216 VAL cc_start: 0.8177 (t) cc_final: 0.7805 (t) REVERT: B 318 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8077 (t) REVERT: B 342 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7297 (pt0) REVERT: B 373 LYS cc_start: 0.7516 (mttt) cc_final: 0.6734 (mttm) REVERT: C 63 LYS cc_start: 0.8564 (pttt) cc_final: 0.8249 (pttp) REVERT: C 265 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6023 (tppt) REVERT: C 373 LYS cc_start: 0.7165 (mttt) cc_final: 0.6666 (mttm) REVERT: D 63 LYS cc_start: 0.8499 (pttt) cc_final: 0.8191 (pttp) REVERT: D 87 LYS cc_start: 0.7286 (mttt) cc_final: 0.6588 (mttm) REVERT: D 145 LEU cc_start: 0.7597 (mp) cc_final: 0.7177 (mt) REVERT: D 161 ILE cc_start: 0.8297 (mt) cc_final: 0.8092 (mm) REVERT: D 216 VAL cc_start: 0.8557 (t) cc_final: 0.8174 (t) REVERT: D 342 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7247 (pt0) REVERT: D 373 LYS cc_start: 0.7275 (mttt) cc_final: 0.6627 (mttm) REVERT: E 63 LYS cc_start: 0.8731 (pttt) cc_final: 0.8255 (pttp) REVERT: E 87 LYS cc_start: 0.7269 (mttt) cc_final: 0.6693 (mttm) REVERT: E 143 ASP cc_start: 0.8654 (p0) cc_final: 0.8452 (p0) REVERT: E 216 VAL cc_start: 0.8177 (t) cc_final: 0.7781 (t) REVERT: E 318 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8085 (t) REVERT: E 342 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7294 (pt0) REVERT: E 373 LYS cc_start: 0.7465 (mttt) cc_final: 0.6706 (mttm) REVERT: F 63 LYS cc_start: 0.8619 (pttt) cc_final: 0.8267 (pttp) REVERT: F 108 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7496 (tppp) REVERT: F 143 ASP cc_start: 0.8963 (p0) cc_final: 0.8636 (p0) REVERT: F 161 ILE cc_start: 0.8310 (mt) cc_final: 0.7923 (mm) REVERT: F 265 LYS cc_start: 0.7315 (mmmt) cc_final: 0.6087 (tppt) REVERT: F 373 LYS cc_start: 0.7249 (mttt) cc_final: 0.6753 (mttm) outliers start: 58 outliers final: 33 residues processed: 335 average time/residue: 0.2592 time to fit residues: 134.9384 Evaluate side-chains 312 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 1.799 ------------------------------------------------------------------------------- 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 213 THR 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 185 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 49 THR 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 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 213 THR 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 185 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 71 VAL 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 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: 246 random chunks: chunk 221 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 212 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN E 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17172 Z= 0.206 Angle : 0.651 9.235 23532 Z= 0.329 Chirality : 0.046 0.145 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.453 22.250 2592 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.59 % Favored : 90.59 % Rotamer: Outliers : 2.97 % Allowed : 14.10 % Favored : 82.93 % 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: -1.98 (0.17), residues: 2178 helix: -0.08 (0.29), residues: 342 sheet: -0.96 (0.17), residues: 720 loop : -1.95 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 105 HIS 0.002 0.001 HIS C 99 PHE 0.013 0.002 PHE E 250 TYR 0.012 0.001 TYR D 208 ARG 0.002 0.000 ARG F 297 *********************** 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 347 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8449 (pttt) cc_final: 0.8163 (pttp) REVERT: A 87 LYS cc_start: 0.7260 (mttt) cc_final: 0.6849 (mttm) REVERT: A 216 VAL cc_start: 0.8493 (t) cc_final: 0.8148 (t) REVERT: A 342 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7194 (pt0) REVERT: A 373 LYS cc_start: 0.7184 (mttt) cc_final: 0.6644 (mttm) REVERT: B 63 LYS cc_start: 0.8678 (pttt) cc_final: 0.8369 (pttp) REVERT: B 87 LYS cc_start: 0.7284 (mttt) cc_final: 0.6718 (mttm) REVERT: B 108 LYS cc_start: 0.7899 (tppp) cc_final: 0.7677 (tppp) REVERT: B 161 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 216 VAL cc_start: 0.8131 (t) cc_final: 0.7791 (t) REVERT: B 220 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6883 (tttp) REVERT: B 265 LYS cc_start: 0.6918 (mptt) cc_final: 0.6691 (mmmm) REVERT: B 318 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8036 (t) REVERT: B 342 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7169 (pt0) REVERT: B 373 LYS cc_start: 0.7553 (mttt) cc_final: 0.6690 (mttm) REVERT: C 63 LYS cc_start: 0.8578 (pttt) cc_final: 0.8243 (pttp) REVERT: C 129 GLU cc_start: 0.6735 (tt0) cc_final: 0.6444 (tp30) REVERT: C 220 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6636 (tttp) REVERT: C 265 LYS cc_start: 0.7126 (mmtt) cc_final: 0.5996 (tppt) REVERT: C 373 LYS cc_start: 0.7274 (mttt) cc_final: 0.6823 (mttm) REVERT: D 63 LYS cc_start: 0.8450 (pttt) cc_final: 0.8166 (pttp) REVERT: D 87 LYS cc_start: 0.7257 (mttt) cc_final: 0.6849 (mttm) REVERT: D 161 ILE cc_start: 0.8204 (mt) cc_final: 0.7997 (mm) REVERT: D 216 VAL cc_start: 0.8509 (t) cc_final: 0.8153 (t) REVERT: D 342 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7189 (pt0) REVERT: D 373 LYS cc_start: 0.7260 (mttt) cc_final: 0.6622 (mttm) REVERT: E 63 LYS cc_start: 0.8688 (pttt) cc_final: 0.8376 (pttp) REVERT: E 87 LYS cc_start: 0.7281 (mttt) cc_final: 0.6721 (mttm) REVERT: E 108 LYS cc_start: 0.7897 (tppp) cc_final: 0.7676 (tppp) REVERT: E 161 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8096 (mp) REVERT: E 216 VAL cc_start: 0.8115 (t) cc_final: 0.7787 (t) REVERT: E 220 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6879 (tttp) REVERT: E 265 LYS cc_start: 0.6926 (mptt) cc_final: 0.6701 (mmmm) REVERT: E 318 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8027 (t) REVERT: E 342 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7165 (pt0) REVERT: E 373 LYS cc_start: 0.7508 (mttt) cc_final: 0.6683 (mttm) REVERT: F 108 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7216 (tppp) REVERT: F 143 ASP cc_start: 0.9011 (p0) cc_final: 0.8714 (p0) REVERT: F 161 ILE cc_start: 0.8248 (mt) cc_final: 0.7886 (mm) REVERT: F 220 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6616 (tttp) REVERT: F 265 LYS cc_start: 0.7367 (mmmt) cc_final: 0.6062 (tppt) REVERT: F 373 LYS cc_start: 0.7264 (mttt) cc_final: 0.6835 (mttm) outliers start: 44 outliers final: 21 residues processed: 320 average time/residue: 0.2652 time to fit residues: 129.1492 Evaluate side-chains 311 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 213 THR 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 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 49 THR 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 D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 213 THR 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 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 61 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 201 GLN D 201 GLN E 201 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17172 Z= 0.354 Angle : 0.750 14.149 23532 Z= 0.373 Chirality : 0.048 0.176 2946 Planarity : 0.006 0.065 3054 Dihedral : 5.639 24.522 2592 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.00 % Favored : 90.17 % Rotamer: Outliers : 4.39 % Allowed : 14.17 % 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: -2.22 (0.17), residues: 2178 helix: -0.20 (0.28), residues: 360 sheet: -1.16 (0.17), residues: 774 loop : -2.16 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 105 HIS 0.003 0.001 HIS E 359 PHE 0.019 0.002 PHE E 250 TYR 0.011 0.001 TYR A 208 ARG 0.003 0.001 ARG D 308 *********************** 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 348 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 283 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8512 (pttt) cc_final: 0.8141 (pttp) REVERT: A 87 LYS cc_start: 0.7312 (mttt) cc_final: 0.6932 (mttm) REVERT: A 216 VAL cc_start: 0.8802 (t) cc_final: 0.8498 (t) REVERT: A 342 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7421 (pt0) REVERT: A 373 LYS cc_start: 0.7165 (mttt) cc_final: 0.6660 (mttm) REVERT: B 63 LYS cc_start: 0.8762 (pttt) cc_final: 0.8233 (pttp) REVERT: B 87 LYS cc_start: 0.7292 (mttt) cc_final: 0.7004 (mmtm) REVERT: B 161 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8167 (mp) REVERT: B 216 VAL cc_start: 0.8463 (t) cc_final: 0.8094 (t) REVERT: B 220 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7205 (tttp) REVERT: B 265 LYS cc_start: 0.7012 (mptt) cc_final: 0.6790 (mmmm) REVERT: B 373 LYS cc_start: 0.7531 (mttt) cc_final: 0.6712 (mttm) REVERT: C 63 LYS cc_start: 0.8615 (pttt) cc_final: 0.8306 (pttp) REVERT: C 129 GLU cc_start: 0.6759 (tt0) cc_final: 0.6462 (tp30) REVERT: C 143 ASP cc_start: 0.8967 (p0) cc_final: 0.8765 (p0) REVERT: C 220 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6799 (tttp) REVERT: C 265 LYS cc_start: 0.7197 (mmtt) cc_final: 0.5908 (tppt) REVERT: C 373 LYS cc_start: 0.7382 (mttt) cc_final: 0.6734 (mttm) REVERT: D 63 LYS cc_start: 0.8518 (pttt) cc_final: 0.8147 (pttp) REVERT: D 87 LYS cc_start: 0.7311 (mttt) cc_final: 0.6961 (mttm) REVERT: D 216 VAL cc_start: 0.8802 (t) cc_final: 0.8488 (t) REVERT: D 293 LYS cc_start: 0.7152 (ptpt) cc_final: 0.6581 (ptpp) REVERT: D 342 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7422 (pt0) REVERT: D 373 LYS cc_start: 0.7215 (mttt) cc_final: 0.6683 (mttm) REVERT: E 63 LYS cc_start: 0.8778 (pttt) cc_final: 0.8235 (pttp) REVERT: E 87 LYS cc_start: 0.7297 (mttt) cc_final: 0.7013 (mmtm) REVERT: E 161 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8171 (mp) REVERT: E 216 VAL cc_start: 0.8460 (t) cc_final: 0.8098 (t) REVERT: E 220 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7192 (tttp) REVERT: E 265 LYS cc_start: 0.7020 (mptt) cc_final: 0.6801 (mmmm) REVERT: E 342 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 373 LYS cc_start: 0.7512 (mttt) cc_final: 0.6707 (mttm) REVERT: F 108 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7345 (ttpp) REVERT: F 220 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6762 (tttp) REVERT: F 265 LYS cc_start: 0.7458 (mmmt) cc_final: 0.7121 (mmtt) REVERT: F 373 LYS cc_start: 0.7401 (mttt) cc_final: 0.6766 (mttm) outliers start: 65 outliers final: 36 residues processed: 327 average time/residue: 0.2721 time to fit residues: 136.1527 Evaluate side-chains 309 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 202 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 LYS 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 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 49 THR 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 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 D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 220 LYS 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 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 49 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 0.0050 chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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: 0.3859 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= 0.205 Angle : 0.662 16.196 23532 Z= 0.329 Chirality : 0.046 0.141 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.191 24.100 2592 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.68 % Favored : 90.59 % Rotamer: Outliers : 3.37 % Allowed : 17.00 % Favored : 79.62 % 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: -1.81 (0.18), residues: 2178 helix: 0.42 (0.29), residues: 360 sheet: -0.92 (0.17), residues: 774 loop : -2.00 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 105 HIS 0.001 0.000 HIS D 83 PHE 0.024 0.002 PHE A 250 TYR 0.013 0.001 TYR A 208 ARG 0.001 0.000 ARG F 369 *********************** 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 341 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8424 (pttt) cc_final: 0.8105 (pttp) REVERT: A 87 LYS cc_start: 0.7293 (mttt) cc_final: 0.6893 (mttm) REVERT: A 216 VAL cc_start: 0.8520 (t) cc_final: 0.8094 (t) REVERT: A 265 LYS cc_start: 0.6714 (mmmt) cc_final: 0.5823 (tppt) REVERT: A 342 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7353 (pt0) REVERT: A 373 LYS cc_start: 0.7118 (mttt) cc_final: 0.6749 (mttm) REVERT: B 63 LYS cc_start: 0.8643 (pttt) cc_final: 0.8369 (pttp) REVERT: B 87 LYS cc_start: 0.7323 (mttt) cc_final: 0.6755 (mttm) REVERT: B 161 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 216 VAL cc_start: 0.8164 (t) cc_final: 0.7778 (t) REVERT: B 220 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6922 (tttp) REVERT: B 373 LYS cc_start: 0.7548 (mttt) cc_final: 0.6724 (mttm) REVERT: C 63 LYS cc_start: 0.8613 (pttt) cc_final: 0.8394 (pttp) REVERT: C 143 ASP cc_start: 0.8958 (p0) cc_final: 0.8727 (p0) REVERT: C 220 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6373 (tttp) REVERT: C 265 LYS cc_start: 0.7096 (mmtt) cc_final: 0.5948 (tppt) REVERT: C 373 LYS cc_start: 0.7207 (mttt) cc_final: 0.6690 (mttm) REVERT: D 63 LYS cc_start: 0.8435 (pttt) cc_final: 0.8107 (pttp) REVERT: D 87 LYS cc_start: 0.7283 (mttt) cc_final: 0.6885 (mttm) REVERT: D 216 VAL cc_start: 0.8534 (t) cc_final: 0.8097 (t) REVERT: D 265 LYS cc_start: 0.6772 (mmmt) cc_final: 0.6012 (tppt) REVERT: D 293 LYS cc_start: 0.6699 (ptpt) cc_final: 0.6228 (ptpp) REVERT: D 342 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7356 (pt0) REVERT: D 373 LYS cc_start: 0.7163 (mttt) cc_final: 0.6795 (mttm) REVERT: E 63 LYS cc_start: 0.8651 (pttt) cc_final: 0.8371 (pttp) REVERT: E 87 LYS cc_start: 0.7324 (mttt) cc_final: 0.6763 (mttm) REVERT: E 161 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8130 (mp) REVERT: E 216 VAL cc_start: 0.8156 (t) cc_final: 0.7769 (t) REVERT: E 220 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6919 (tttp) REVERT: E 342 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7131 (pt0) REVERT: E 373 LYS cc_start: 0.7522 (mttt) cc_final: 0.6721 (mttm) REVERT: F 108 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7214 (ttpp) REVERT: F 161 ILE cc_start: 0.8243 (mt) cc_final: 0.8005 (mp) REVERT: F 220 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6329 (tttp) REVERT: F 265 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6877 (mmtt) REVERT: F 373 LYS cc_start: 0.7214 (mttt) cc_final: 0.6705 (mttm) outliers start: 50 outliers final: 27 residues processed: 321 average time/residue: 0.2631 time to fit residues: 129.2745 Evaluate side-chains 311 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 220 LYS Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 49 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 324 ASN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 49 THR 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 216 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 324 ASN 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 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 49 THR 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 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: 246 random chunks: chunk 229 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17172 Z= 0.461 Angle : 0.798 14.968 23532 Z= 0.397 Chirality : 0.049 0.221 2946 Planarity : 0.006 0.067 3054 Dihedral : 5.689 24.485 2592 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.32 % Favored : 89.85 % Rotamer: Outliers : 4.66 % Allowed : 16.26 % 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: -2.17 (0.17), residues: 2178 helix: 0.14 (0.28), residues: 360 sheet: -1.21 (0.17), residues: 774 loop : -2.17 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP E 219 HIS 0.002 0.001 HIS B 359 PHE 0.032 0.002 PHE D 250 TYR 0.013 0.002 TYR A 181 ARG 0.004 0.001 ARG C 196 *********************** 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 326 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 257 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8531 (pttt) cc_final: 0.8254 (pttp) REVERT: A 265 LYS cc_start: 0.6969 (mmmt) cc_final: 0.6143 (tppt) REVERT: A 342 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7376 (pt0) REVERT: A 373 LYS cc_start: 0.7155 (mttt) cc_final: 0.6716 (mttm) REVERT: B 63 LYS cc_start: 0.8782 (pttt) cc_final: 0.8258 (pttp) REVERT: B 87 LYS cc_start: 0.7358 (mttt) cc_final: 0.6855 (mttm) REVERT: B 161 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 220 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7219 (tttp) REVERT: B 265 LYS cc_start: 0.7541 (mmmm) cc_final: 0.6413 (tppt) REVERT: B 373 LYS cc_start: 0.7519 (mttt) cc_final: 0.6629 (mttm) REVERT: C 63 LYS cc_start: 0.8640 (pttt) cc_final: 0.8350 (pttp) REVERT: C 143 ASP cc_start: 0.9026 (p0) cc_final: 0.8790 (p0) REVERT: C 220 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6787 (tttp) REVERT: C 265 LYS cc_start: 0.7251 (mmtt) cc_final: 0.6039 (tppt) REVERT: C 373 LYS cc_start: 0.7325 (mttt) cc_final: 0.6686 (mttm) REVERT: D 63 LYS cc_start: 0.8540 (pttt) cc_final: 0.8234 (pttp) REVERT: D 342 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7377 (pt0) REVERT: D 373 LYS cc_start: 0.7215 (mttt) cc_final: 0.6716 (mttm) REVERT: E 63 LYS cc_start: 0.8782 (pttt) cc_final: 0.8253 (pttp) REVERT: E 87 LYS cc_start: 0.7355 (mttt) cc_final: 0.6862 (mttm) REVERT: E 161 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.7972 (mp) REVERT: E 216 VAL cc_start: 0.8568 (t) cc_final: 0.8310 (t) REVERT: E 220 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7227 (tttp) REVERT: E 265 LYS cc_start: 0.7550 (mmmm) cc_final: 0.6423 (tppt) REVERT: E 373 LYS cc_start: 0.7476 (mttt) cc_final: 0.6617 (mttm) REVERT: F 108 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7518 (ttpp) REVERT: F 220 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6550 (tttp) REVERT: F 265 LYS cc_start: 0.7422 (mmmt) cc_final: 0.7108 (tttm) REVERT: F 373 LYS cc_start: 0.7332 (mttt) cc_final: 0.6590 (mttm) outliers start: 69 outliers final: 38 residues processed: 311 average time/residue: 0.2829 time to fit residues: 134.8174 Evaluate side-chains 299 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 254 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 102 THR Chi-restraints excluded: chain A residue 213 THR 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 B residue 48 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 213 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 49 THR 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 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 D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 48 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 213 THR Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 49 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.6806 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17172 Z= 0.188 Angle : 0.666 18.102 23532 Z= 0.331 Chirality : 0.046 0.141 2946 Planarity : 0.005 0.063 3054 Dihedral : 5.123 23.460 2592 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.54 % Favored : 90.73 % Rotamer: Outliers : 2.29 % Allowed : 18.96 % Favored : 78.74 % 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: -1.71 (0.18), residues: 2178 helix: 0.66 (0.30), residues: 360 sheet: -0.91 (0.17), residues: 774 loop : -1.96 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 105 HIS 0.001 0.000 HIS C 83 PHE 0.018 0.002 PHE A 218 TYR 0.014 0.001 TYR A 208 ARG 0.002 0.000 ARG F 369 *********************** 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 337 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 303 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8463 (pttt) cc_final: 0.8188 (pttp) REVERT: A 215 ASN cc_start: 0.6016 (m-40) cc_final: 0.5603 (m-40) REVERT: A 216 VAL cc_start: 0.8553 (t) cc_final: 0.8183 (t) REVERT: A 265 LYS cc_start: 0.6749 (mmmt) cc_final: 0.6037 (tppt) REVERT: A 342 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7270 (pt0) REVERT: A 373 LYS cc_start: 0.7168 (mttt) cc_final: 0.6796 (mttm) REVERT: B 63 LYS cc_start: 0.8677 (pttt) cc_final: 0.8232 (pttp) REVERT: B 87 LYS cc_start: 0.7331 (mttt) cc_final: 0.6925 (mttm) REVERT: B 127 TYR cc_start: 0.9277 (p90) cc_final: 0.8978 (p90) REVERT: B 216 VAL cc_start: 0.8154 (t) cc_final: 0.7791 (t) REVERT: B 220 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6871 (tttp) REVERT: B 373 LYS cc_start: 0.7554 (mttt) cc_final: 0.6731 (mttm) REVERT: C 143 ASP cc_start: 0.8960 (p0) cc_final: 0.8720 (p0) REVERT: C 220 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6389 (tttp) REVERT: C 265 LYS cc_start: 0.7004 (mmtt) cc_final: 0.5844 (tppt) REVERT: C 373 LYS cc_start: 0.7186 (mttt) cc_final: 0.6572 (mttm) REVERT: D 63 LYS cc_start: 0.8473 (pttt) cc_final: 0.8167 (pttp) REVERT: D 215 ASN cc_start: 0.6015 (m-40) cc_final: 0.5606 (m-40) REVERT: D 216 VAL cc_start: 0.8562 (t) cc_final: 0.8185 (t) REVERT: D 265 LYS cc_start: 0.6766 (mmmt) cc_final: 0.5853 (tppt) REVERT: D 342 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7270 (pt0) REVERT: D 373 LYS cc_start: 0.7191 (mttt) cc_final: 0.6850 (mttm) REVERT: E 63 LYS cc_start: 0.8686 (pttt) cc_final: 0.8239 (pttp) REVERT: E 87 LYS cc_start: 0.7334 (mttt) cc_final: 0.6922 (mttm) REVERT: E 127 TYR cc_start: 0.9279 (p90) cc_final: 0.8992 (p90) REVERT: E 216 VAL cc_start: 0.8163 (t) cc_final: 0.7799 (t) REVERT: E 220 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6866 (tttp) REVERT: E 373 LYS cc_start: 0.7529 (mttt) cc_final: 0.6712 (mttm) REVERT: F 108 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7152 (ttpp) REVERT: F 220 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6294 (tttp) REVERT: F 265 LYS cc_start: 0.7254 (mmmt) cc_final: 0.6953 (mmtt) REVERT: F 373 LYS cc_start: 0.7168 (mttt) cc_final: 0.6578 (mttm) outliers start: 34 outliers final: 17 residues processed: 330 average time/residue: 0.2871 time to fit residues: 144.2279 Evaluate side-chains 313 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 220 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 277 ILE 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 C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 230 SER 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 220 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 0.9980 chunk 227 optimal weight: 0.0030 chunk 207 optimal weight: 0.5980 chunk 220 optimal weight: 0.0980 chunk 132 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 145 optimal weight: 0.0870 overall best weight: 0.3568 ------------------------------------------------------------------------------- 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: 0.6745 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17172 Z= 0.167 Angle : 0.649 16.579 23532 Z= 0.323 Chirality : 0.045 0.152 2946 Planarity : 0.005 0.061 3054 Dihedral : 4.771 23.677 2592 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.86 % Favored : 90.31 % Rotamer: Outliers : 2.23 % Allowed : 19.10 % Favored : 78.68 % 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: -1.42 (0.18), residues: 2178 helix: 0.93 (0.30), residues: 360 sheet: -0.70 (0.17), residues: 774 loop : -1.80 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 105 HIS 0.001 0.000 HIS D 99 PHE 0.013 0.001 PHE A 250 TYR 0.016 0.001 TYR A 181 ARG 0.003 0.000 ARG D 334 *********************** 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 361 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASN cc_start: 0.6153 (m-40) cc_final: 0.5629 (m110) REVERT: A 216 VAL cc_start: 0.8468 (t) cc_final: 0.8043 (t) REVERT: A 265 LYS cc_start: 0.6743 (mmmt) cc_final: 0.5931 (tppt) REVERT: A 342 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7126 (pt0) REVERT: A 373 LYS cc_start: 0.7141 (mttt) cc_final: 0.6812 (mttm) REVERT: B 87 LYS cc_start: 0.7304 (mttt) cc_final: 0.6805 (mmtm) REVERT: B 108 LYS cc_start: 0.7732 (tppp) cc_final: 0.7514 (tptm) REVERT: B 161 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 216 VAL cc_start: 0.7921 (t) cc_final: 0.7552 (t) REVERT: B 220 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6604 (tttp) REVERT: B 373 LYS cc_start: 0.7562 (mttt) cc_final: 0.6731 (mttm) REVERT: C 143 ASP cc_start: 0.8832 (p0) cc_final: 0.8561 (p0) REVERT: C 220 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6082 (tttp) REVERT: C 265 LYS cc_start: 0.6982 (mmtt) cc_final: 0.5925 (tppt) REVERT: C 373 LYS cc_start: 0.7421 (mttt) cc_final: 0.6835 (mttm) REVERT: D 63 LYS cc_start: 0.8353 (pttt) cc_final: 0.8153 (pttp) REVERT: D 215 ASN cc_start: 0.6159 (m-40) cc_final: 0.5642 (m110) REVERT: D 216 VAL cc_start: 0.8474 (t) cc_final: 0.8031 (t) REVERT: D 265 LYS cc_start: 0.6810 (mmmt) cc_final: 0.6048 (tppt) REVERT: D 342 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7124 (pt0) REVERT: D 373 LYS cc_start: 0.7166 (mttt) cc_final: 0.6816 (mttm) REVERT: E 87 LYS cc_start: 0.7296 (mttt) cc_final: 0.6808 (mmtm) REVERT: E 108 LYS cc_start: 0.7730 (tppp) cc_final: 0.7511 (tptm) REVERT: E 161 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7626 (mp) REVERT: E 216 VAL cc_start: 0.7924 (t) cc_final: 0.7554 (t) REVERT: E 220 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6608 (tttp) REVERT: E 373 LYS cc_start: 0.7516 (mttt) cc_final: 0.6712 (mttm) REVERT: F 161 ILE cc_start: 0.8182 (mt) cc_final: 0.7962 (mp) REVERT: F 220 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.5950 (pttp) REVERT: F 265 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6664 (mmtt) REVERT: F 373 LYS cc_start: 0.7447 (mttt) cc_final: 0.6855 (mttm) outliers start: 33 outliers final: 19 residues processed: 348 average time/residue: 0.2702 time to fit residues: 142.5004 Evaluate side-chains 311 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 286 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 150 optimal weight: 0.0060 chunk 119 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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: 0.6849 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17172 Z= 0.338 Angle : 0.750 16.359 23532 Z= 0.371 Chirality : 0.048 0.198 2946 Planarity : 0.006 0.065 3054 Dihedral : 5.153 22.622 2592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.92 % Favored : 89.35 % Rotamer: Outliers : 2.50 % Allowed : 18.89 % Favored : 78.61 % 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: -1.64 (0.18), residues: 2178 helix: 0.66 (0.29), residues: 360 sheet: -0.85 (0.17), residues: 774 loop : -1.90 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 219 HIS 0.002 0.001 HIS D 99 PHE 0.023 0.002 PHE A 250 TYR 0.030 0.002 TYR A 271 ARG 0.005 0.000 ARG D 334 ********************** 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 319 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.6816 (mmmt) cc_final: 0.5858 (tppt) REVERT: A 342 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7383 (pt0) REVERT: A 373 LYS cc_start: 0.7141 (mttt) cc_final: 0.6777 (mttm) REVERT: B 87 LYS cc_start: 0.7254 (mttt) cc_final: 0.6878 (mttm) REVERT: B 161 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.7177 (mp) REVERT: B 216 VAL cc_start: 0.8306 (t) cc_final: 0.7938 (t) REVERT: B 220 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6991 (tttp) REVERT: B 373 LYS cc_start: 0.7540 (mttt) cc_final: 0.6727 (mttm) REVERT: C 220 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6730 (tttp) REVERT: C 265 LYS cc_start: 0.7049 (mmtt) cc_final: 0.5960 (tppt) REVERT: C 373 LYS cc_start: 0.7249 (mttt) cc_final: 0.6627 (mttm) REVERT: D 63 LYS cc_start: 0.8512 (pttt) cc_final: 0.8190 (pttp) REVERT: D 216 VAL cc_start: 0.8802 (t) cc_final: 0.8393 (t) REVERT: D 265 LYS cc_start: 0.6876 (mmmt) cc_final: 0.6050 (tppt) REVERT: D 293 LYS cc_start: 0.7439 (mttt) cc_final: 0.7226 (mtpt) REVERT: D 342 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7392 (pt0) REVERT: D 373 LYS cc_start: 0.7163 (mttt) cc_final: 0.6773 (mttm) REVERT: E 87 LYS cc_start: 0.7261 (mttt) cc_final: 0.6869 (mttm) REVERT: E 161 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.7184 (mp) REVERT: E 216 VAL cc_start: 0.8312 (t) cc_final: 0.7944 (t) REVERT: E 220 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6995 (tttp) REVERT: E 373 LYS cc_start: 0.7499 (mttt) cc_final: 0.6779 (mttm) REVERT: F 220 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6577 (tttp) REVERT: F 373 LYS cc_start: 0.7228 (mttt) cc_final: 0.6601 (mttm) outliers start: 37 outliers final: 23 residues processed: 307 average time/residue: 0.2760 time to fit residues: 127.7288 Evaluate side-chains 295 residues out of total 1878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 213 THR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 213 THR 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 161 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 220 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101355 restraints weight = 30412.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103232 restraints weight = 22325.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104424 restraints weight = 17986.493| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17172 Z= 0.318 Angle : 0.748 16.291 23532 Z= 0.370 Chirality : 0.047 0.165 2946 Planarity : 0.006 0.065 3054 Dihedral : 5.228 22.315 2592 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.06 % Favored : 89.21 % Rotamer: Outliers : 2.23 % Allowed : 19.37 % Favored : 78.41 % 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: -1.75 (0.18), residues: 2178 helix: 0.64 (0.29), residues: 360 sheet: -0.95 (0.17), residues: 774 loop : -1.97 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 219 HIS 0.002 0.001 HIS A 99 PHE 0.020 0.002 PHE D 218 TYR 0.032 0.002 TYR D 271 ARG 0.005 0.000 ARG D 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.05 seconds wall clock time: 58 minutes 57.73 seconds (3537.73 seconds total)