Starting phenix.real_space_refine on Mon Jul 22 13:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pn2_17768/07_2024/8pn2_17768_neut.cif" } resolution = 2.63 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= 0.074 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 72 5.16 5 C 11676 2.51 5 N 3216 2.21 5 O 3510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 18498 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "F" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3051 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.90, per 1000 atoms: 0.59 Number of scatterers: 18498 At special positions: 0 Unit cell: (125.46, 124.64, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 18 15.00 Mg 6 11.99 O 3510 8.00 N 3216 7.00 C 11676 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: 6.88 Conformation dependent library (CDL) restraints added in 3.4 seconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 24.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.625A pdb=" N TYR A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 446 through 460 removed outlier: 3.512A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 4.015A pdb=" N TYR B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 73 " --> pdb=" O TYR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.594A pdb=" N PHE B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 73 removed outlier: 3.707A pdb=" N TYR C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 446 through 459 removed outlier: 3.539A pdb=" N PHE C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 73 removed outlier: 3.702A pdb=" N TYR D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.538A pdb=" N PHE D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 73 removed outlier: 4.042A pdb=" N TYR E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU E 73 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 327 through 331 Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 446 through 459 removed outlier: 3.576A pdb=" N PHE E 459 " --> pdb=" O GLN E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 72 removed outlier: 3.562A pdb=" N TYR F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 186 through 194 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 327 through 331 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 432 through 440 Processing helix chain 'F' and resid 446 through 460 removed outlier: 3.513A pdb=" N PHE F 459 " --> pdb=" O GLN F 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 3.718A pdb=" N ARG D 265 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 3.611A pdb=" N GLY A 114 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILE A 129 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 122 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 127 " --> pdb=" O ARG A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 136 current: chain 'A' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 172 current: chain 'A' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 286 through 288 current: chain 'A' and resid 345 through 358 removed outlier: 5.750A pdb=" N THR A 349 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY A 373 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 351 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 371 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 353 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 369 " --> pdb=" O TYR A 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 364 through 373 current: chain 'A' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 400 through 405 current: chain 'A' and resid 424 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443 removed outlier: 3.731A pdb=" N ARG A 265 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 247 removed outlier: 3.595A pdb=" N GLY A 261 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.792A pdb=" N ARG E 265 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 122 removed outlier: 3.589A pdb=" N GLY B 114 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 129 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ARG B 122 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR B 127 " --> pdb=" O ARG B 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 136 current: chain 'B' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 170 current: chain 'B' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 286 through 288 current: chain 'B' and resid 344 through 358 removed outlier: 5.794A pdb=" N THR B 349 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY B 373 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET B 351 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 371 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR B 353 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 369 " --> pdb=" O TYR B 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 373 current: chain 'B' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 400 through 405 current: chain 'B' and resid 424 through 431 Processing sheet with id=AA8, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'B' and resid 441 through 443 removed outlier: 3.790A pdb=" N ARG B 265 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 245 through 247 removed outlier: 3.526A pdb=" N GLY B 261 " --> pdb=" O MET B 246 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.742A pdb=" N ARG F 265 " --> pdb=" O PHE F 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 122 removed outlier: 5.216A pdb=" N ILE C 129 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG C 122 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR C 127 " --> pdb=" O ARG C 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 136 current: chain 'C' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 170 current: chain 'C' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 288 current: chain 'C' and resid 344 through 358 removed outlier: 5.753A pdb=" N THR C 349 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY C 373 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET C 351 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 371 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 353 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 369 " --> pdb=" O TYR C 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 364 through 373 current: chain 'C' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 400 through 405 current: chain 'C' and resid 424 through 431 Processing sheet with id=AB4, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AB5, first strand: chain 'C' and resid 441 through 443 removed outlier: 3.728A pdb=" N ARG C 265 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 245 through 247 removed outlier: 3.561A pdb=" N GLY C 261 " --> pdb=" O MET C 246 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 122 removed outlier: 5.215A pdb=" N ILE D 129 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG D 122 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR D 127 " --> pdb=" O ARG D 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 136 current: chain 'D' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 172 current: chain 'D' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 286 through 288 current: chain 'D' and resid 345 through 358 removed outlier: 5.694A pdb=" N THR D 349 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY D 373 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET D 351 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 371 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR D 353 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 369 " --> pdb=" O TYR D 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 373 current: chain 'D' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 400 through 405 current: chain 'D' and resid 424 through 431 Processing sheet with id=AB8, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB9, first strand: chain 'D' and resid 245 through 247 removed outlier: 3.512A pdb=" N GLY D 261 " --> pdb=" O MET D 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 114 through 122 removed outlier: 3.588A pdb=" N GLY E 114 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE E 129 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ARG E 122 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR E 127 " --> pdb=" O ARG E 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 136 current: chain 'E' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 172 current: chain 'E' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 286 through 288 current: chain 'E' and resid 344 through 358 removed outlier: 5.748A pdb=" N THR E 349 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY E 373 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET E 351 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL E 371 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 353 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 369 " --> pdb=" O TYR E 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 364 through 373 current: chain 'E' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 400 through 405 current: chain 'E' and resid 424 through 431 Processing sheet with id=AC2, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AC3, first strand: chain 'E' and resid 245 through 247 Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 122 removed outlier: 3.563A pdb=" N GLY F 114 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE F 129 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ARG F 122 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N THR F 127 " --> pdb=" O ARG F 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 125 through 136 current: chain 'F' and resid 162 through 170 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 170 current: chain 'F' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 286 through 288 current: chain 'F' and resid 344 through 358 removed outlier: 5.732A pdb=" N THR F 349 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY F 373 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET F 351 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL F 371 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR F 353 " --> pdb=" O ILE F 369 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 369 " --> pdb=" O TYR F 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 364 through 373 current: chain 'F' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 400 through 405 current: chain 'F' and resid 424 through 431 Processing sheet with id=AC5, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AC6, first strand: chain 'F' and resid 245 through 247 removed outlier: 3.570A pdb=" N GLY F 261 " --> pdb=" O MET F 246 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1173 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: 6.04 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6167 1.34 - 1.46: 4311 1.46 - 1.58: 8296 1.58 - 1.70: 24 1.70 - 1.81: 96 Bond restraints: 18894 Sorted by residual: bond pdb=" CA ILE E 129 " pdb=" C ILE E 129 " ideal model delta sigma weight residual 1.524 1.511 0.013 8.30e-03 1.45e+04 2.52e+00 bond pdb=" N ASP F 128 " pdb=" CA ASP F 128 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.96e+00 bond pdb=" N ASP A 128 " pdb=" CA ASP A 128 " ideal model delta sigma weight residual 1.460 1.476 -0.016 1.54e-02 4.22e+03 1.14e+00 bond pdb=" CA ASP A 128 " pdb=" CB ASP A 128 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.08e+00 bond pdb=" CA ASP F 128 " pdb=" CB ASP F 128 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.36e-01 ... (remaining 18889 not shown) Histogram of bond angle deviations from ideal: 100.79 - 108.61: 1076 108.61 - 116.43: 12173 116.43 - 124.26: 11943 124.26 - 132.08: 428 132.08 - 139.90: 54 Bond angle restraints: 25674 Sorted by residual: angle pdb=" N GLY D 257 " pdb=" CA GLY D 257 " pdb=" C GLY D 257 " ideal model delta sigma weight residual 110.38 115.63 -5.25 1.48e+00 4.57e-01 1.26e+01 angle pdb=" N GLY E 194 " pdb=" CA GLY E 194 " pdb=" C GLY E 194 " ideal model delta sigma weight residual 113.18 119.91 -6.73 2.37e+00 1.78e-01 8.06e+00 angle pdb=" N GLY A 194 " pdb=" CA GLY A 194 " pdb=" C GLY A 194 " ideal model delta sigma weight residual 113.18 119.79 -6.61 2.37e+00 1.78e-01 7.78e+00 angle pdb=" N GLY C 194 " pdb=" CA GLY C 194 " pdb=" C GLY C 194 " ideal model delta sigma weight residual 113.18 119.79 -6.61 2.37e+00 1.78e-01 7.77e+00 angle pdb=" N GLY B 194 " pdb=" CA GLY B 194 " pdb=" C GLY B 194 " ideal model delta sigma weight residual 113.18 119.72 -6.54 2.37e+00 1.78e-01 7.62e+00 ... (remaining 25669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 10060 17.79 - 35.59: 871 35.59 - 53.38: 147 53.38 - 71.18: 77 71.18 - 88.97: 29 Dihedral angle restraints: 11184 sinusoidal: 4536 harmonic: 6648 Sorted by residual: dihedral pdb=" CA MET C 184 " pdb=" C MET C 184 " pdb=" N PHE C 185 " pdb=" CA PHE C 185 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP F 368 " pdb=" CB ASP F 368 " pdb=" CG ASP F 368 " pdb=" OD1 ASP F 368 " ideal model delta sinusoidal sigma weight residual -30.00 -88.69 58.69 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA MET A 184 " pdb=" C MET A 184 " pdb=" N PHE A 185 " pdb=" CA PHE A 185 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 11181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2121 0.040 - 0.079: 457 0.079 - 0.119: 240 0.119 - 0.159: 31 0.159 - 0.198: 7 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CG LEU D 239 " pdb=" CB LEU D 239 " pdb=" CD1 LEU D 239 " pdb=" CD2 LEU D 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU A 239 " pdb=" CB LEU A 239 " pdb=" CD1 LEU A 239 " pdb=" CD2 LEU A 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CG LEU E 239 " pdb=" CB LEU E 239 " pdb=" CD1 LEU E 239 " pdb=" CD2 LEU E 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 2853 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 144 " -0.016 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP E 144 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP E 144 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP E 144 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 144 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 144 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 144 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 146 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO F 147 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 147 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 147 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 127 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C THR A 127 " -0.024 2.00e-02 2.50e+03 pdb=" O THR A 127 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 128 " 0.008 2.00e-02 2.50e+03 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 266 2.55 - 3.14: 14334 3.14 - 3.73: 31010 3.73 - 4.31: 44876 4.31 - 4.90: 73220 Nonbonded interactions: 163706 Sorted by model distance: nonbonded pdb=" OD1 ASP A 166 " pdb="MG MG A1002 " model vdw 1.969 2.170 nonbonded pdb=" OD1 ASP F 166 " pdb="MG MG F1002 " model vdw 1.970 2.170 nonbonded pdb=" OD1 ASP B 166 " pdb="MG MG B1002 " model vdw 1.977 2.170 nonbonded pdb=" OD1 ASP E 166 " pdb="MG MG E1002 " model vdw 1.984 2.170 nonbonded pdb=" O ILE A 121 " pdb="MG MG A1002 " model vdw 1.984 2.170 ... (remaining 163701 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 51.020 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.003 0.036 18894 Z= 0.169 Angle : 0.515 6.728 25674 Z= 0.272 Chirality : 0.043 0.198 2856 Planarity : 0.003 0.039 3318 Dihedral : 15.375 88.972 6948 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.05 % Allowed : 1.58 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2334 helix: -0.23 (0.26), residues: 402 sheet: -0.32 (0.21), residues: 510 loop : 0.12 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 144 HIS 0.007 0.001 HIS B 421 PHE 0.017 0.001 PHE E 111 TYR 0.020 0.001 TYR F 69 ARG 0.008 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7893 (m-80) cc_final: 0.7585 (m-80) REVERT: A 184 MET cc_start: 0.7034 (ppp) cc_final: 0.6707 (ppp) REVERT: A 416 LYS cc_start: 0.8276 (tptm) cc_final: 0.7211 (mptt) REVERT: A 438 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7324 (tpp-160) REVERT: B 197 GLU cc_start: 0.7641 (pt0) cc_final: 0.7134 (pm20) REVERT: B 224 ASN cc_start: 0.7045 (m110) cc_final: 0.6075 (t0) REVERT: B 241 TYR cc_start: 0.8283 (t80) cc_final: 0.8011 (t80) REVERT: B 259 TYR cc_start: 0.8103 (t80) cc_final: 0.7153 (t80) REVERT: B 452 ASP cc_start: 0.7138 (t0) cc_final: 0.6932 (t70) REVERT: C 122 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8034 (ttp-110) REVERT: C 164 ASP cc_start: 0.7387 (m-30) cc_final: 0.6914 (p0) REVERT: C 209 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7645 (pt0) REVERT: C 224 ASN cc_start: 0.7124 (m110) cc_final: 0.6154 (t0) REVERT: C 320 LYS cc_start: 0.8181 (tttp) cc_final: 0.7723 (ttpt) REVERT: D 164 ASP cc_start: 0.7383 (m-30) cc_final: 0.7000 (p0) REVERT: D 224 ASN cc_start: 0.7082 (m110) cc_final: 0.6257 (t0) REVERT: D 285 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7809 (mm-30) REVERT: D 320 LYS cc_start: 0.8153 (tttp) cc_final: 0.7768 (ttpt) REVERT: E 224 ASN cc_start: 0.7089 (m110) cc_final: 0.6067 (t0) REVERT: E 259 TYR cc_start: 0.8273 (t80) cc_final: 0.7566 (t80) REVERT: F 164 ASP cc_start: 0.7255 (m-30) cc_final: 0.6874 (p0) REVERT: F 241 TYR cc_start: 0.8436 (t80) cc_final: 0.7949 (t80) REVERT: F 416 LYS cc_start: 0.8289 (tptm) cc_final: 0.7240 (mptt) REVERT: F 438 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7327 (tpp-160) outliers start: 1 outliers final: 2 residues processed: 341 average time/residue: 1.1725 time to fit residues: 454.0853 Evaluate side-chains 265 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.0060 chunk 177 optimal weight: 0.0670 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 0.0020 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 0.0870 overall best weight: 0.0498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 325 GLN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN E 243 ASN F 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18894 Z= 0.144 Angle : 0.475 5.628 25674 Z= 0.248 Chirality : 0.043 0.141 2856 Planarity : 0.003 0.028 3318 Dihedral : 9.275 87.001 2752 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.03 % Allowed : 9.15 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2334 helix: -0.13 (0.25), residues: 438 sheet: -0.05 (0.22), residues: 468 loop : 0.28 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 144 HIS 0.003 0.000 HIS D 421 PHE 0.025 0.001 PHE D 211 TYR 0.015 0.001 TYR F 69 ARG 0.004 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 297 time to evaluate : 1.904 Fit side-chains REVERT: A 111 PHE cc_start: 0.7912 (m-80) cc_final: 0.7652 (m-80) REVERT: A 184 MET cc_start: 0.6909 (ppp) cc_final: 0.6619 (ppp) REVERT: A 224 ASN cc_start: 0.7224 (m110) cc_final: 0.6409 (t0) REVERT: A 438 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.7305 (tpp-160) REVERT: A 452 ASP cc_start: 0.7505 (t0) cc_final: 0.6946 (t0) REVERT: B 197 GLU cc_start: 0.7667 (pt0) cc_final: 0.7130 (pm20) REVERT: B 224 ASN cc_start: 0.6955 (m110) cc_final: 0.5986 (t0) REVERT: B 259 TYR cc_start: 0.7944 (t80) cc_final: 0.6949 (t80) REVERT: B 363 ILE cc_start: 0.7903 (mt) cc_final: 0.7608 (mp) REVERT: C 164 ASP cc_start: 0.7300 (m-30) cc_final: 0.6876 (p0) REVERT: C 209 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7649 (pt0) REVERT: C 224 ASN cc_start: 0.6928 (m110) cc_final: 0.5916 (t0) REVERT: C 285 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 320 LYS cc_start: 0.8034 (tttp) cc_final: 0.7677 (ttpt) REVERT: C 325 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6642 (mp-120) REVERT: C 367 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8038 (m) REVERT: D 164 ASP cc_start: 0.7350 (m-30) cc_final: 0.6951 (p0) REVERT: D 224 ASN cc_start: 0.7044 (m110) cc_final: 0.6185 (t0) REVERT: D 285 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 325 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6621 (mp-120) REVERT: D 456 GLN cc_start: 0.7161 (tp40) cc_final: 0.6810 (mm110) REVERT: E 224 ASN cc_start: 0.7056 (m110) cc_final: 0.6032 (t0) REVERT: E 259 TYR cc_start: 0.8169 (t80) cc_final: 0.7536 (t80) REVERT: F 64 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: F 224 ASN cc_start: 0.7208 (m110) cc_final: 0.6358 (t0) REVERT: F 241 TYR cc_start: 0.8356 (t80) cc_final: 0.7909 (t80) REVERT: F 416 LYS cc_start: 0.8218 (tptm) cc_final: 0.7168 (mptt) REVERT: F 438 ARG cc_start: 0.7545 (mmt-90) cc_final: 0.7289 (tpp-160) outliers start: 40 outliers final: 11 residues processed: 307 average time/residue: 1.1961 time to fit residues: 419.5586 Evaluate side-chains 266 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 0.3980 chunk 229 optimal weight: 0.8980 chunk 189 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN B 243 ASN C 243 ASN C 325 GLN D 243 ASN D 325 GLN E 243 ASN F 325 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18894 Z= 0.172 Angle : 0.476 5.809 25674 Z= 0.249 Chirality : 0.043 0.135 2856 Planarity : 0.003 0.029 3318 Dihedral : 8.646 86.216 2748 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.18 % Allowed : 11.38 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2334 helix: 0.05 (0.25), residues: 438 sheet: -0.06 (0.22), residues: 468 loop : 0.35 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 144 HIS 0.003 0.001 HIS F 141 PHE 0.025 0.001 PHE D 211 TYR 0.011 0.001 TYR D 69 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 258 time to evaluate : 2.266 Fit side-chains REVERT: A 64 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: A 111 PHE cc_start: 0.7956 (m-80) cc_final: 0.7693 (m-80) REVERT: A 224 ASN cc_start: 0.7213 (m110) cc_final: 0.6332 (t0) REVERT: A 325 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6560 (mp-120) REVERT: A 416 LYS cc_start: 0.8265 (tptm) cc_final: 0.7255 (mptt) REVERT: A 438 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.7295 (tpp-160) REVERT: A 452 ASP cc_start: 0.7578 (t70) cc_final: 0.7037 (t0) REVERT: B 64 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: B 123 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7750 (mppt) REVERT: B 197 GLU cc_start: 0.7680 (pt0) cc_final: 0.7151 (pm20) REVERT: B 224 ASN cc_start: 0.6956 (m110) cc_final: 0.5945 (t0) REVERT: B 259 TYR cc_start: 0.8090 (t80) cc_final: 0.7077 (t80) REVERT: B 452 ASP cc_start: 0.7300 (t0) cc_final: 0.7097 (t0) REVERT: C 164 ASP cc_start: 0.7328 (m-30) cc_final: 0.6861 (p0) REVERT: C 209 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7653 (pt0) REVERT: C 224 ASN cc_start: 0.6937 (m110) cc_final: 0.5906 (t0) REVERT: C 285 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 320 LYS cc_start: 0.8105 (tttp) cc_final: 0.7709 (ttpt) REVERT: C 456 GLN cc_start: 0.6929 (tp40) cc_final: 0.6624 (mm110) REVERT: D 224 ASN cc_start: 0.7069 (m110) cc_final: 0.6194 (t0) REVERT: D 421 HIS cc_start: 0.6423 (OUTLIER) cc_final: 0.6092 (t-170) REVERT: D 456 GLN cc_start: 0.7187 (tp40) cc_final: 0.6788 (mm110) REVERT: E 224 ASN cc_start: 0.7060 (m110) cc_final: 0.6034 (t0) REVERT: E 259 TYR cc_start: 0.8284 (t80) cc_final: 0.7602 (t80) REVERT: E 452 ASP cc_start: 0.7289 (t0) cc_final: 0.7076 (t0) REVERT: F 64 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: F 125 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: F 224 ASN cc_start: 0.7200 (m110) cc_final: 0.6284 (t0) REVERT: F 241 TYR cc_start: 0.8459 (t80) cc_final: 0.8068 (t80) REVERT: F 416 LYS cc_start: 0.8302 (tptm) cc_final: 0.7260 (mptt) REVERT: F 438 ARG cc_start: 0.7544 (mmt-90) cc_final: 0.7267 (tpp-160) outliers start: 43 outliers final: 22 residues processed: 279 average time/residue: 1.0063 time to fit residues: 325.5228 Evaluate side-chains 264 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 chunk 101 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 ASN C 325 GLN D 243 ASN D 325 GLN E 243 ASN F 325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18894 Z= 0.165 Angle : 0.471 6.021 25674 Z= 0.247 Chirality : 0.042 0.138 2856 Planarity : 0.003 0.045 3318 Dihedral : 8.276 88.067 2748 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.39 % Allowed : 12.50 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2334 helix: 0.12 (0.25), residues: 438 sheet: -0.05 (0.22), residues: 468 loop : 0.37 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 144 HIS 0.003 0.001 HIS F 141 PHE 0.026 0.001 PHE D 211 TYR 0.020 0.001 TYR F 69 ARG 0.007 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 1.854 Fit side-chains REVERT: A 64 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: A 111 PHE cc_start: 0.7983 (m-80) cc_final: 0.7754 (m-80) REVERT: A 184 MET cc_start: 0.6771 (ppp) cc_final: 0.6474 (ppp) REVERT: A 224 ASN cc_start: 0.7213 (m110) cc_final: 0.6332 (t0) REVERT: A 241 TYR cc_start: 0.8265 (t80) cc_final: 0.8056 (t80) REVERT: A 416 LYS cc_start: 0.8240 (tptm) cc_final: 0.7254 (mptt) REVERT: A 438 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.7287 (tpp-160) REVERT: A 452 ASP cc_start: 0.7560 (t70) cc_final: 0.7026 (t0) REVERT: B 64 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6430 (pp20) REVERT: B 123 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7745 (mppt) REVERT: B 197 GLU cc_start: 0.7726 (pt0) cc_final: 0.7162 (pm20) REVERT: B 224 ASN cc_start: 0.6972 (m110) cc_final: 0.5981 (t0) REVERT: B 259 TYR cc_start: 0.8121 (t80) cc_final: 0.7097 (t80) REVERT: C 209 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7651 (pt0) REVERT: C 224 ASN cc_start: 0.6895 (m110) cc_final: 0.5841 (t0) REVERT: C 285 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 320 LYS cc_start: 0.8136 (tttp) cc_final: 0.7733 (ttpt) REVERT: C 367 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8037 (m) REVERT: C 456 GLN cc_start: 0.6992 (tp40) cc_final: 0.6701 (mm110) REVERT: D 224 ASN cc_start: 0.7075 (m110) cc_final: 0.6175 (t0) REVERT: D 285 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 421 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.6026 (t-170) REVERT: D 452 ASP cc_start: 0.7329 (t0) cc_final: 0.7036 (t0) REVERT: D 456 GLN cc_start: 0.7178 (tp40) cc_final: 0.6843 (mm110) REVERT: E 64 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: E 146 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6700 (m-40) REVERT: E 224 ASN cc_start: 0.7084 (m110) cc_final: 0.6052 (t0) REVERT: E 259 TYR cc_start: 0.8281 (t80) cc_final: 0.7641 (t80) REVERT: F 64 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6120 (mp0) REVERT: F 125 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: F 184 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6591 (mtm) REVERT: F 224 ASN cc_start: 0.7187 (m110) cc_final: 0.6274 (t0) REVERT: F 325 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6548 (mp-120) REVERT: F 416 LYS cc_start: 0.8276 (tptm) cc_final: 0.7288 (mptt) REVERT: F 438 ARG cc_start: 0.7496 (mmt-90) cc_final: 0.7212 (tpp-160) outliers start: 47 outliers final: 22 residues processed: 279 average time/residue: 1.0562 time to fit residues: 339.3497 Evaluate side-chains 269 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 6.9990 chunk 128 optimal weight: 0.0030 chunk 3 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.7930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN C 243 ASN D 325 GLN E 243 ASN F 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18894 Z= 0.191 Angle : 0.483 5.884 25674 Z= 0.254 Chirality : 0.043 0.130 2856 Planarity : 0.003 0.060 3318 Dihedral : 8.150 84.622 2748 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.85 % Allowed : 13.47 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2334 helix: 0.15 (0.25), residues: 438 sheet: -0.07 (0.22), residues: 468 loop : 0.38 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 144 HIS 0.003 0.001 HIS F 248 PHE 0.023 0.001 PHE C 211 TYR 0.010 0.001 TYR C 259 ARG 0.007 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 252 time to evaluate : 1.917 Fit side-chains REVERT: A 64 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: A 111 PHE cc_start: 0.7988 (m-80) cc_final: 0.7773 (m-80) REVERT: A 125 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: A 184 MET cc_start: 0.6773 (ppp) cc_final: 0.6467 (ppp) REVERT: A 224 ASN cc_start: 0.7208 (m110) cc_final: 0.6310 (t0) REVERT: A 241 TYR cc_start: 0.8391 (t80) cc_final: 0.7966 (t80) REVERT: A 414 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7799 (tpp80) REVERT: A 416 LYS cc_start: 0.8324 (tptm) cc_final: 0.7283 (mptt) REVERT: A 438 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7250 (tpp-160) REVERT: A 452 ASP cc_start: 0.7549 (t70) cc_final: 0.7012 (t0) REVERT: B 64 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: B 123 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7752 (mppt) REVERT: B 197 GLU cc_start: 0.7727 (pt0) cc_final: 0.7144 (pm20) REVERT: B 224 ASN cc_start: 0.6995 (m110) cc_final: 0.5966 (t0) REVERT: B 259 TYR cc_start: 0.8160 (t80) cc_final: 0.7134 (t80) REVERT: C 209 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7656 (pt0) REVERT: C 224 ASN cc_start: 0.6913 (m110) cc_final: 0.5861 (t0) REVERT: C 243 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8505 (p0) REVERT: C 254 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (mp) REVERT: C 285 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 320 LYS cc_start: 0.8167 (tttp) cc_final: 0.7759 (ttpt) REVERT: C 452 ASP cc_start: 0.7459 (t0) cc_final: 0.7163 (t0) REVERT: C 456 GLN cc_start: 0.6980 (tp40) cc_final: 0.6700 (mm110) REVERT: D 224 ASN cc_start: 0.7074 (m110) cc_final: 0.6205 (t0) REVERT: D 285 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7865 (mt-10) REVERT: D 325 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6889 (mp-120) REVERT: D 456 GLN cc_start: 0.7189 (tp40) cc_final: 0.6841 (mm110) REVERT: E 64 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6537 (pp20) REVERT: E 146 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6782 (m-40) REVERT: E 224 ASN cc_start: 0.7106 (m110) cc_final: 0.6075 (t0) REVERT: E 259 TYR cc_start: 0.8319 (t80) cc_final: 0.7721 (t80) REVERT: F 64 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: F 125 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: F 184 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6620 (mtm) REVERT: F 224 ASN cc_start: 0.7181 (m110) cc_final: 0.6231 (t0) REVERT: F 241 TYR cc_start: 0.8509 (t80) cc_final: 0.8126 (t80) REVERT: F 414 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7791 (tpp80) REVERT: F 416 LYS cc_start: 0.8384 (tptm) cc_final: 0.7334 (mptt) REVERT: F 438 ARG cc_start: 0.7467 (mmt-90) cc_final: 0.7233 (tpp-160) outliers start: 56 outliers final: 23 residues processed: 284 average time/residue: 1.0866 time to fit residues: 353.7279 Evaluate side-chains 276 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.6980 chunk 203 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN D 325 GLN E 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18894 Z= 0.282 Angle : 0.542 6.317 25674 Z= 0.286 Chirality : 0.045 0.139 2856 Planarity : 0.004 0.037 3318 Dihedral : 8.488 84.071 2748 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.56 % Allowed : 14.13 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2334 helix: -0.01 (0.25), residues: 438 sheet: -0.15 (0.21), residues: 468 loop : 0.29 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 144 HIS 0.005 0.001 HIS F 248 PHE 0.027 0.002 PHE D 211 TYR 0.022 0.001 TYR A 69 ARG 0.006 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 2.182 Fit side-chains REVERT: A 64 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: A 111 PHE cc_start: 0.7995 (m-80) cc_final: 0.7775 (m-80) REVERT: A 123 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7820 (mppt) REVERT: A 125 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: A 224 ASN cc_start: 0.7233 (m110) cc_final: 0.6316 (t0) REVERT: A 241 TYR cc_start: 0.8515 (t80) cc_final: 0.7850 (t80) REVERT: A 414 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7836 (tpp80) REVERT: A 416 LYS cc_start: 0.8473 (tptm) cc_final: 0.7342 (mptt) REVERT: A 438 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.7274 (tpp-160) REVERT: A 452 ASP cc_start: 0.7546 (t70) cc_final: 0.7027 (t0) REVERT: B 64 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: B 123 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7793 (mppt) REVERT: B 125 ASP cc_start: 0.6987 (p0) cc_final: 0.6414 (m-30) REVERT: B 224 ASN cc_start: 0.7028 (m110) cc_final: 0.5995 (t0) REVERT: B 259 TYR cc_start: 0.8349 (t80) cc_final: 0.7386 (t80) REVERT: C 209 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7670 (pt0) REVERT: C 224 ASN cc_start: 0.6973 (m110) cc_final: 0.5862 (t0) REVERT: C 320 LYS cc_start: 0.8148 (tttp) cc_final: 0.7726 (ttpt) REVERT: C 452 ASP cc_start: 0.7387 (t0) cc_final: 0.7181 (t0) REVERT: C 456 GLN cc_start: 0.7015 (tp40) cc_final: 0.6724 (mm110) REVERT: D 224 ASN cc_start: 0.7072 (m110) cc_final: 0.6217 (t0) REVERT: D 325 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6865 (mp-120) REVERT: D 456 GLN cc_start: 0.7231 (tp40) cc_final: 0.6824 (mm110) REVERT: E 64 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: E 146 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6859 (m-40) REVERT: E 224 ASN cc_start: 0.7126 (m110) cc_final: 0.6085 (t0) REVERT: F 64 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: F 125 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: F 184 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6650 (mtm) REVERT: F 224 ASN cc_start: 0.7187 (m110) cc_final: 0.6240 (t0) REVERT: F 241 TYR cc_start: 0.8556 (t80) cc_final: 0.8125 (t80) REVERT: F 414 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7841 (tpp80) REVERT: F 416 LYS cc_start: 0.8468 (tptm) cc_final: 0.7342 (mptt) REVERT: F 438 ARG cc_start: 0.7501 (mmt-90) cc_final: 0.7246 (tpp-160) outliers start: 70 outliers final: 31 residues processed: 271 average time/residue: 1.1597 time to fit residues: 359.4707 Evaluate side-chains 266 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 455 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 165 optimal weight: 0.3980 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 243 ASN C 325 GLN D 325 GLN E 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18894 Z= 0.211 Angle : 0.506 6.064 25674 Z= 0.267 Chirality : 0.043 0.146 2856 Planarity : 0.003 0.037 3318 Dihedral : 8.255 87.291 2748 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.30 % Allowed : 15.24 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2334 helix: -0.01 (0.25), residues: 438 sheet: -0.15 (0.22), residues: 468 loop : 0.29 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 144 HIS 0.003 0.001 HIS A 248 PHE 0.026 0.002 PHE D 211 TYR 0.011 0.001 TYR D 259 ARG 0.007 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 235 time to evaluate : 2.096 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: A 111 PHE cc_start: 0.8003 (m-80) cc_final: 0.7792 (m-80) REVERT: A 125 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: A 224 ASN cc_start: 0.7192 (m110) cc_final: 0.6260 (t0) REVERT: A 241 TYR cc_start: 0.8505 (t80) cc_final: 0.8022 (t80) REVERT: A 414 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7808 (tpp80) REVERT: A 416 LYS cc_start: 0.8385 (tptm) cc_final: 0.7312 (mptt) REVERT: A 438 ARG cc_start: 0.7511 (mmt-90) cc_final: 0.7254 (tpp-160) REVERT: A 452 ASP cc_start: 0.7534 (t70) cc_final: 0.7027 (t0) REVERT: B 64 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: B 123 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7786 (mppt) REVERT: B 224 ASN cc_start: 0.7007 (m110) cc_final: 0.5979 (t0) REVERT: B 259 TYR cc_start: 0.8308 (t80) cc_final: 0.7331 (t80) REVERT: C 209 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7657 (pt0) REVERT: C 224 ASN cc_start: 0.6947 (m110) cc_final: 0.5840 (t0) REVERT: C 320 LYS cc_start: 0.8291 (tttp) cc_final: 0.7857 (ttpt) REVERT: C 325 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6976 (mp-120) REVERT: C 456 GLN cc_start: 0.6983 (tp40) cc_final: 0.6704 (mm110) REVERT: D 224 ASN cc_start: 0.7065 (m110) cc_final: 0.6158 (t0) REVERT: D 456 GLN cc_start: 0.7193 (tp40) cc_final: 0.6809 (mm110) REVERT: E 64 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: E 146 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6834 (m-40) REVERT: E 224 ASN cc_start: 0.7115 (m110) cc_final: 0.6070 (t0) REVERT: F 64 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: F 125 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: F 184 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6629 (mtm) REVERT: F 224 ASN cc_start: 0.7187 (m110) cc_final: 0.6221 (t0) REVERT: F 414 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7814 (tpp80) REVERT: F 416 LYS cc_start: 0.8453 (tptm) cc_final: 0.7349 (mptt) outliers start: 65 outliers final: 34 residues processed: 276 average time/residue: 1.1519 time to fit residues: 362.4621 Evaluate side-chains 273 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 455 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 205 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN E 243 ASN F 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18894 Z= 0.201 Angle : 0.503 6.547 25674 Z= 0.265 Chirality : 0.043 0.131 2856 Planarity : 0.003 0.037 3318 Dihedral : 8.089 88.318 2748 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.30 % Allowed : 15.24 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2334 helix: -0.02 (0.25), residues: 438 sheet: -0.06 (0.22), residues: 462 loop : 0.27 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 275 HIS 0.002 0.001 HIS F 248 PHE 0.025 0.001 PHE D 211 TYR 0.011 0.001 TYR C 259 ARG 0.007 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 237 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: A 111 PHE cc_start: 0.8010 (m-80) cc_final: 0.7802 (m-80) REVERT: A 125 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: A 184 MET cc_start: 0.6836 (ppp) cc_final: 0.6555 (ppp) REVERT: A 224 ASN cc_start: 0.7201 (m110) cc_final: 0.6265 (t0) REVERT: A 414 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7798 (tpp80) REVERT: A 416 LYS cc_start: 0.8387 (tptm) cc_final: 0.7309 (mptt) REVERT: A 452 ASP cc_start: 0.7537 (t70) cc_final: 0.7036 (t0) REVERT: B 64 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 123 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7849 (mppt) REVERT: B 224 ASN cc_start: 0.7012 (m110) cc_final: 0.5987 (t0) REVERT: B 259 TYR cc_start: 0.8292 (t80) cc_final: 0.7233 (t80) REVERT: C 209 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7645 (pt0) REVERT: C 224 ASN cc_start: 0.6942 (m110) cc_final: 0.5842 (t0) REVERT: C 320 LYS cc_start: 0.8229 (tttp) cc_final: 0.7828 (ttpt) REVERT: C 325 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6886 (mp-120) REVERT: C 452 ASP cc_start: 0.7296 (t0) cc_final: 0.7019 (t0) REVERT: C 456 GLN cc_start: 0.6980 (tp40) cc_final: 0.6683 (mm110) REVERT: D 224 ASN cc_start: 0.7072 (m110) cc_final: 0.6128 (t0) REVERT: D 452 ASP cc_start: 0.7267 (t0) cc_final: 0.7016 (t0) REVERT: D 456 GLN cc_start: 0.7191 (tp40) cc_final: 0.6805 (mm110) REVERT: E 64 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: E 146 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6856 (m-40) REVERT: E 224 ASN cc_start: 0.7115 (m110) cc_final: 0.6070 (t0) REVERT: F 64 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: F 125 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: F 224 ASN cc_start: 0.7237 (m110) cc_final: 0.6244 (t0) REVERT: F 414 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (tpp80) REVERT: F 416 LYS cc_start: 0.8457 (tptm) cc_final: 0.7344 (mptt) outliers start: 65 outliers final: 42 residues processed: 280 average time/residue: 1.0697 time to fit residues: 344.0340 Evaluate side-chains 280 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 455 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN E 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 18894 Z= 0.418 Angle : 0.628 7.166 25674 Z= 0.332 Chirality : 0.048 0.146 2856 Planarity : 0.005 0.047 3318 Dihedral : 9.080 87.772 2748 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 15.14 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2334 helix: 0.04 (0.26), residues: 402 sheet: -0.58 (0.21), residues: 498 loop : 0.24 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 275 HIS 0.008 0.002 HIS A 248 PHE 0.024 0.002 PHE D 211 TYR 0.023 0.002 TYR F 69 ARG 0.007 0.001 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 222 time to evaluate : 2.062 Fit side-chains REVERT: A 64 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: A 111 PHE cc_start: 0.7982 (m-80) cc_final: 0.7748 (m-80) REVERT: A 125 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: A 224 ASN cc_start: 0.7329 (m110) cc_final: 0.6407 (t0) REVERT: A 241 TYR cc_start: 0.8598 (t80) cc_final: 0.8068 (t80) REVERT: A 377 GLN cc_start: 0.8041 (mt0) cc_final: 0.7726 (mt0) REVERT: A 414 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: A 416 LYS cc_start: 0.8424 (tptm) cc_final: 0.7318 (mptt) REVERT: B 64 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: B 123 LYS cc_start: 0.8469 (mmtt) cc_final: 0.7861 (mppt) REVERT: B 125 ASP cc_start: 0.6997 (p0) cc_final: 0.6415 (m-30) REVERT: B 224 ASN cc_start: 0.7174 (m110) cc_final: 0.6055 (t0) REVERT: B 259 TYR cc_start: 0.8437 (t80) cc_final: 0.7636 (t80) REVERT: C 209 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7695 (pt0) REVERT: C 224 ASN cc_start: 0.7042 (m110) cc_final: 0.6058 (t0) REVERT: C 320 LYS cc_start: 0.8252 (tttp) cc_final: 0.7803 (ttpt) REVERT: C 325 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6875 (mp-120) REVERT: C 456 GLN cc_start: 0.7038 (tp40) cc_final: 0.6670 (mm110) REVERT: D 224 ASN cc_start: 0.7105 (m110) cc_final: 0.6201 (t0) REVERT: D 456 GLN cc_start: 0.7265 (tp40) cc_final: 0.6802 (mm110) REVERT: E 64 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: E 146 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6893 (m-40) REVERT: E 224 ASN cc_start: 0.7243 (m110) cc_final: 0.6113 (t0) REVERT: F 125 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: F 184 MET cc_start: 0.6806 (mtm) cc_final: 0.6531 (ptt) REVERT: F 224 ASN cc_start: 0.7304 (m110) cc_final: 0.6342 (t0) REVERT: F 377 GLN cc_start: 0.8157 (mt0) cc_final: 0.7852 (mt0) REVERT: F 414 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7893 (ttp80) REVERT: F 416 LYS cc_start: 0.8480 (tptm) cc_final: 0.7348 (mptt) REVERT: F 421 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6018 (t-90) outliers start: 69 outliers final: 41 residues processed: 271 average time/residue: 1.0172 time to fit residues: 318.2236 Evaluate side-chains 269 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 455 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 421 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 243 ASN C 325 GLN E 243 ASN E 421 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18894 Z= 0.212 Angle : 0.530 6.209 25674 Z= 0.280 Chirality : 0.044 0.136 2856 Planarity : 0.003 0.045 3318 Dihedral : 8.427 88.000 2748 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.69 % Allowed : 16.36 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2334 helix: -0.20 (0.24), residues: 438 sheet: -0.28 (0.22), residues: 468 loop : 0.18 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 144 HIS 0.002 0.001 HIS F 248 PHE 0.024 0.002 PHE D 211 TYR 0.011 0.001 TYR D 259 ARG 0.007 0.000 ARG B 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 2.036 Fit side-chains REVERT: A 64 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: A 111 PHE cc_start: 0.8019 (m-80) cc_final: 0.7795 (m-80) REVERT: A 224 ASN cc_start: 0.7275 (m110) cc_final: 0.6325 (t0) REVERT: A 241 TYR cc_start: 0.8508 (t80) cc_final: 0.7730 (t80) REVERT: A 414 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7827 (tpp80) REVERT: A 416 LYS cc_start: 0.8406 (tptm) cc_final: 0.7331 (mptt) REVERT: A 452 ASP cc_start: 0.7621 (t0) cc_final: 0.7170 (t0) REVERT: B 64 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: B 123 LYS cc_start: 0.8464 (mmtt) cc_final: 0.7851 (mppt) REVERT: B 224 ASN cc_start: 0.7064 (m110) cc_final: 0.6034 (t0) REVERT: B 259 TYR cc_start: 0.8339 (t80) cc_final: 0.7381 (t80) REVERT: B 320 LYS cc_start: 0.7599 (tttm) cc_final: 0.7311 (ttpt) REVERT: C 209 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7667 (pt0) REVERT: C 224 ASN cc_start: 0.7027 (m110) cc_final: 0.6017 (t0) REVERT: C 320 LYS cc_start: 0.8313 (tttp) cc_final: 0.7881 (ttpt) REVERT: C 452 ASP cc_start: 0.7308 (t0) cc_final: 0.7024 (t0) REVERT: C 456 GLN cc_start: 0.6999 (tp40) cc_final: 0.6661 (mm110) REVERT: D 224 ASN cc_start: 0.7070 (m110) cc_final: 0.6170 (t0) REVERT: D 452 ASP cc_start: 0.7171 (t0) cc_final: 0.6941 (t0) REVERT: D 456 GLN cc_start: 0.7203 (tp40) cc_final: 0.6791 (mm110) REVERT: E 64 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: E 224 ASN cc_start: 0.7124 (m110) cc_final: 0.6059 (t0) REVERT: E 363 ILE cc_start: 0.8186 (mt) cc_final: 0.7835 (mp) REVERT: F 64 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: F 125 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: F 184 MET cc_start: 0.6744 (mtm) cc_final: 0.6540 (ptt) REVERT: F 224 ASN cc_start: 0.7259 (m110) cc_final: 0.6272 (t0) REVERT: F 414 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7827 (tpp80) REVERT: F 416 LYS cc_start: 0.8477 (tptm) cc_final: 0.7370 (mptt) outliers start: 53 outliers final: 37 residues processed: 264 average time/residue: 1.0151 time to fit residues: 309.3744 Evaluate side-chains 267 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 455 GLN Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 455 GLN Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 414 ARG Chi-restraints excluded: chain F residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 171 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 243 ASN E 421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153514 restraints weight = 20184.611| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.74 r_work: 0.3740 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 18894 Z= 0.239 Angle : 0.714 59.198 25674 Z= 0.411 Chirality : 0.046 0.763 2856 Planarity : 0.003 0.044 3318 Dihedral : 8.444 88.022 2748 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 2.44 % Allowed : 16.87 % Favored : 80.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2334 helix: -0.19 (0.24), residues: 438 sheet: -0.18 (0.22), residues: 462 loop : 0.15 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 144 HIS 0.002 0.001 HIS D 141 PHE 0.023 0.001 PHE D 211 TYR 0.011 0.001 TYR D 259 ARG 0.006 0.000 ARG E 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6397.18 seconds wall clock time: 113 minutes 42.89 seconds (6822.89 seconds total)