Starting phenix.real_space_refine on Tue Dec 31 20:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzb_36741/12_2024/8jzb_36741.cif" } resolution = 2.76 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= -0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 Na 6 4.78 5 C 10548 2.51 5 N 2713 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "D" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "F" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "H" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.94, per 1000 atoms: 0.66 Number of scatterers: 16660 At special positions: 0 Unit cell: (151.11, 146.73, 139.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 Na 6 11.00 O 3285 8.00 N 2713 7.00 C 10548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS H 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.05 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 568 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS F 188 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 285 " - pdb=" SG CYS F 298 " distance=2.03 Simple disulfide: pdb=" SG CYS F 494 " - pdb=" SG CYS F 506 " distance=2.03 Simple disulfide: pdb=" SG CYS F 568 " - pdb=" SG CYS F 577 " distance=2.03 Simple disulfide: pdb=" SG CYS H 188 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 285 " - pdb=" SG CYS H 298 " distance=2.03 Simple disulfide: pdb=" SG CYS H 384 " - pdb=" SG CYS H 502 " distance=2.03 Simple disulfide: pdb=" SG CYS H 494 " - pdb=" SG CYS H 506 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 577 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 701 " - " ASN B 192 " " NAG C 1 " - " ASN D 189 " " NAG E 1 " - " ASN F 189 " " NAG G 1 " - " ASN H 189 " Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 2.4 seconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 25 sheets defined 19.4% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.517A pdb=" N LEU B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.758A pdb=" N VAL B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.791A pdb=" N THR B 478 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 99 removed outlier: 3.532A pdb=" N VAL D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'F' and resid 62 through 99 removed outlier: 3.725A pdb=" N THR F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 113 through 141 Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 391 through 400 removed outlier: 3.718A pdb=" N VAL F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 437 removed outlier: 3.769A pdb=" N SER F 437 " --> pdb=" O PRO F 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 99 removed outlier: 4.648A pdb=" N LYS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 113 through 141 Processing helix chain 'H' and resid 162 through 169 removed outlier: 3.599A pdb=" N ASP H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 391 through 400 removed outlier: 3.782A pdb=" N VAL H 400 " --> pdb=" O CYS H 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 177 through 178 current: chain 'B' and resid 560 through 571 removed outlier: 5.531A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 218 through 227 removed outlier: 6.521A pdb=" N SER B 235 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 225 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET B 233 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE B 227 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 248 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 251 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER B 275 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 253 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 273 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 255 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 282 through 290 removed outlier: 3.751A pdb=" N SER B 284 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 339 current: chain 'B' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 360 through 370 current: chain 'B' and resid 405 through 418 Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 448 removed outlier: 4.238A pdb=" N ARG B 466 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 515 through 516 removed outlier: 4.529A pdb=" N SER B 538 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 193 through 199 current: chain 'D' and resid 574 through 584 removed outlier: 4.336A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 227 removed outlier: 6.338A pdb=" N SER D 235 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE D 225 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET D 233 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE D 227 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS D 240 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE D 248 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE D 251 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER D 275 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE D 253 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL D 273 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 255 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.617A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 316 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 339 current: chain 'D' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 360 through 370 current: chain 'D' and resid 405 through 418 Processing sheet with id=AB2, first strand: chain 'D' and resid 443 through 448 Processing sheet with id=AB3, first strand: chain 'D' and resid 514 through 516 removed outlier: 4.545A pdb=" N SER D 538 " --> pdb=" O ILE D 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 177 through 178 current: chain 'F' and resid 560 through 571 removed outlier: 5.526A pdb=" N ILE F 561 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG F 584 " --> pdb=" O ILE F 561 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER F 563 " --> pdb=" O GLU F 582 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU F 582 " --> pdb=" O SER F 563 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 575 " --> pdb=" O VAL F 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 218 through 227 removed outlier: 6.532A pdb=" N SER F 235 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE F 225 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET F 233 " --> pdb=" O PHE F 225 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE F 227 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 231 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER F 250 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS F 240 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 248 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE F 251 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER F 275 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE F 253 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 273 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 255 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 282 through 289 removed outlier: 6.640A pdb=" N SER F 299 " --> pdb=" O ASN F 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS F 285 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 297 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL F 287 " --> pdb=" O TRP F 295 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 295 " --> pdb=" O VAL F 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 339 current: chain 'F' and resid 360 through 369 Processing sheet with id=AB8, first strand: chain 'F' and resid 401 through 402 removed outlier: 5.737A pdb=" N SER F 408 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 443 through 448 Processing sheet with id=AC1, first strand: chain 'F' and resid 514 through 516 removed outlier: 4.338A pdb=" N SER F 538 " --> pdb=" O ILE F 554 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 575 through 584 removed outlier: 4.289A pdb=" N ILE H 575 " --> pdb=" O VAL H 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 218 through 227 removed outlier: 6.514A pdb=" N SER H 235 " --> pdb=" O PRO H 223 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE H 225 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET H 233 " --> pdb=" O PHE H 225 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE H 227 " --> pdb=" O ILE H 231 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE H 231 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR H 232 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU H 255 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE H 234 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE H 253 " --> pdb=" O PHE H 234 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN H 236 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE H 251 " --> pdb=" O GLN H 236 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE H 238 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 257 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL H 259 " --> pdb=" O ALA H 268 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA H 268 " --> pdb=" O VAL H 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 282 through 289 removed outlier: 4.169A pdb=" N SER H 284 " --> pdb=" O SER H 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 338 through 340 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 338 through 340 current: chain 'H' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 360 through 370 current: chain 'H' and resid 405 through 418 Processing sheet with id=AC6, first strand: chain 'H' and resid 443 through 448 removed outlier: 4.212A pdb=" N ARG H 466 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER H 477 " --> pdb=" O PRO H 471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 515 through 516 removed outlier: 4.275A pdb=" N SER H 538 " --> pdb=" O ILE H 554 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5290 1.34 - 1.47: 4256 1.47 - 1.61: 7316 1.61 - 1.74: 0 1.74 - 1.88: 152 Bond restraints: 17014 Sorted by residual: bond pdb=" CA ARG D 239 " pdb=" C ARG D 239 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.21e-02 6.83e+03 1.52e+01 bond pdb=" CA ALA D 550 " pdb=" C ALA D 550 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.21e+01 bond pdb=" CA TYR D 455 " pdb=" C TYR D 455 " ideal model delta sigma weight residual 1.521 1.480 0.041 1.19e-02 7.06e+03 1.18e+01 bond pdb=" CA ALA D 457 " pdb=" C ALA D 457 " ideal model delta sigma weight residual 1.528 1.491 0.037 1.08e-02 8.57e+03 1.16e+01 bond pdb=" C LEU B 555 " pdb=" O LEU B 555 " ideal model delta sigma weight residual 1.233 1.217 0.016 4.80e-03 4.34e+04 1.13e+01 ... (remaining 17009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 22479 2.81 - 5.63: 503 5.63 - 8.44: 80 8.44 - 11.25: 15 11.25 - 14.07: 10 Bond angle restraints: 23087 Sorted by residual: angle pdb=" N ASN B 189 " pdb=" CA ASN B 189 " pdb=" C ASN B 189 " ideal model delta sigma weight residual 111.28 124.52 -13.24 1.09e+00 8.42e-01 1.48e+02 angle pdb=" C ASP H 485 " pdb=" N PRO H 486 " pdb=" CA PRO H 486 " ideal model delta sigma weight residual 119.90 108.57 11.33 1.05e+00 9.07e-01 1.16e+02 angle pdb=" N TRP B 461 " pdb=" CA TRP B 461 " pdb=" C TRP B 461 " ideal model delta sigma weight residual 111.28 122.47 -11.19 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N TRP D 461 " pdb=" CA TRP D 461 " pdb=" C TRP D 461 " ideal model delta sigma weight residual 111.28 122.11 -10.83 1.09e+00 8.42e-01 9.86e+01 angle pdb=" N TRP F 461 " pdb=" CA TRP F 461 " pdb=" C TRP F 461 " ideal model delta sigma weight residual 111.28 121.58 -10.30 1.09e+00 8.42e-01 8.93e+01 ... (remaining 23082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 9383 23.82 - 47.65: 763 47.65 - 71.47: 169 71.47 - 95.30: 51 95.30 - 119.12: 24 Dihedral angle restraints: 10390 sinusoidal: 4242 harmonic: 6148 Sorted by residual: dihedral pdb=" CB CYS D 384 " pdb=" SG CYS D 384 " pdb=" SG CYS D 502 " pdb=" CB CYS D 502 " ideal model delta sinusoidal sigma weight residual 93.00 -177.24 -89.76 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS H 188 " pdb=" SG CYS H 188 " pdb=" SG CYS H 604 " pdb=" CB CYS H 604 " ideal model delta sinusoidal sigma weight residual -86.00 -158.39 72.39 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS H 384 " pdb=" SG CYS H 384 " pdb=" SG CYS H 502 " pdb=" CB CYS H 502 " ideal model delta sinusoidal sigma weight residual -86.00 -147.46 61.46 1 1.00e+01 1.00e-02 5.01e+01 ... (remaining 10387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 2586 0.179 - 0.358: 21 0.358 - 0.537: 4 0.537 - 0.716: 2 0.716 - 0.895: 3 Chirality restraints: 2616 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.15e+03 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 189 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN H 189 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.97e+01 ... (remaining 2613 not shown) Planarity restraints: 2953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.338 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG A 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.113 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " 0.203 2.00e-02 2.50e+03 1.67e-01 3.50e+02 pdb=" C7 NAG B 701 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " -0.270 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 485 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO D 486 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 486 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 486 " 0.052 5.00e-02 4.00e+02 ... (remaining 2950 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3351 2.77 - 3.30: 14936 3.30 - 3.84: 26978 3.84 - 4.37: 32212 4.37 - 4.90: 56909 Nonbonded interactions: 134386 Sorted by model distance: nonbonded pdb=" O ASP H 165 " pdb=" OG1 THR H 168 " model vdw 2.240 3.040 nonbonded pdb=" N GLN F 373 " pdb=" OE1 GLN F 373 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU B 483 " pdb=" NZ LYS B 543 " model vdw 2.287 3.120 nonbonded pdb=" O ILE B 68 " pdb=" NE2 GLN B 72 " model vdw 2.298 3.120 nonbonded pdb=" N GLU H 308 " pdb=" OE1 GLU H 308 " model vdw 2.299 3.120 ... (remaining 134381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 61 through 607) selection = (chain 'D' and resid 61 through 607) selection = (chain 'F' and resid 61 through 607) selection = (chain 'H' and resid 61 through 607) } 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: 0.010 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.900 Find NCS groups from input model: 0.990 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: 0.010 Load rotamer database and sin/cos tables:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 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 : 0.007 0.070 17014 Z= 0.428 Angle : 1.016 14.066 23087 Z= 0.665 Chirality : 0.065 0.895 2616 Planarity : 0.008 0.293 2949 Dihedral : 19.237 119.119 6405 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.14 % Favored : 97.72 % Rotamer: Outliers : 6.93 % Allowed : 19.40 % Favored : 73.67 % 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: 0.59 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 364 sheet: 1.34 (0.19), residues: 754 loop : -1.47 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 461 HIS 0.006 0.001 HIS B 596 PHE 0.017 0.002 PHE H 126 TYR 0.034 0.002 TYR B 446 ARG 0.005 0.000 ARG H 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 98 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8869 (m) REVERT: B 359 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 603 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7826 (mtt) REVERT: D 83 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7044 (p0) REVERT: D 501 MET cc_start: 0.9042 (mmt) cc_final: 0.8327 (mmm) REVERT: F 460 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8775 (p) REVERT: H 78 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7936 (mp) outliers start: 130 outliers final: 40 residues processed: 210 average time/residue: 1.3091 time to fit residues: 310.8411 Evaluate side-chains 123 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN B 359 ASN B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 263 GLN D 430 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN F 430 GLN H 64 ASN H 70 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 591 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17014 Z= 0.319 Angle : 0.656 13.926 23087 Z= 0.334 Chirality : 0.055 0.785 2616 Planarity : 0.004 0.051 2949 Dihedral : 12.292 86.537 2548 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.05 % Allowed : 20.90 % Favored : 75.05 % 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: 0.51 (0.18), residues: 2104 helix: 2.82 (0.27), residues: 367 sheet: 1.29 (0.19), residues: 753 loop : -1.52 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.002 0.001 HIS B 194 PHE 0.041 0.002 PHE D 403 TYR 0.014 0.001 TYR B 571 ARG 0.006 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 77 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: B 603 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: D 93 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8787 (t0) REVERT: D 501 MET cc_start: 0.9093 (mmt) cc_final: 0.8302 (mmm) REVERT: F 501 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: H 93 ASP cc_start: 0.8754 (t0) cc_final: 0.8541 (t0) outliers start: 76 outliers final: 30 residues processed: 144 average time/residue: 1.2074 time to fit residues: 197.7573 Evaluate side-chains 109 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 501 MET Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 191 optimal weight: 0.0980 chunk 65 optimal weight: 0.0670 chunk 154 optimal weight: 0.7980 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN F 71 GLN F 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17014 Z= 0.161 Angle : 0.591 13.639 23087 Z= 0.295 Chirality : 0.051 0.727 2616 Planarity : 0.004 0.043 2949 Dihedral : 10.698 87.235 2497 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.83 % Allowed : 21.16 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2104 helix: 2.97 (0.27), residues: 368 sheet: 1.30 (0.19), residues: 753 loop : -1.47 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 PHE 0.041 0.001 PHE D 403 TYR 0.013 0.001 TYR D 452 ARG 0.005 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 82 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7888 (ptm160) REVERT: F 501 MET cc_start: 0.8697 (mtt) cc_final: 0.8444 (mmm) REVERT: H 93 ASP cc_start: 0.8831 (t0) cc_final: 0.8626 (t0) outliers start: 53 outliers final: 23 residues processed: 127 average time/residue: 1.2542 time to fit residues: 180.4595 Evaluate side-chains 97 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.0040 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17014 Z= 0.175 Angle : 0.568 13.117 23087 Z= 0.284 Chirality : 0.050 0.693 2616 Planarity : 0.004 0.039 2949 Dihedral : 9.598 86.470 2484 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 21.11 % Favored : 76.12 % 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: 0.54 (0.18), residues: 2104 helix: 2.94 (0.27), residues: 368 sheet: 1.30 (0.19), residues: 744 loop : -1.51 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.002 0.000 HIS D 312 PHE 0.035 0.001 PHE D 403 TYR 0.011 0.001 TYR H 446 ARG 0.006 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 75 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8691 (ptp) cc_final: 0.8391 (ppp) REVERT: B 451 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7930 (ptm160) REVERT: D 313 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (mpp) REVERT: F 142 THR cc_start: 0.5915 (OUTLIER) cc_final: 0.5643 (p) REVERT: F 313 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8580 (mmp) outliers start: 52 outliers final: 18 residues processed: 119 average time/residue: 1.1909 time to fit residues: 161.6987 Evaluate side-chains 95 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 GLN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17014 Z= 0.330 Angle : 0.600 12.708 23087 Z= 0.305 Chirality : 0.051 0.666 2616 Planarity : 0.004 0.039 2949 Dihedral : 9.367 85.674 2483 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 20.20 % Favored : 76.65 % 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: 0.46 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 369 sheet: 1.21 (0.19), residues: 746 loop : -1.55 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 576 HIS 0.003 0.001 HIS B 194 PHE 0.017 0.001 PHE B 126 TYR 0.015 0.001 TYR H 446 ARG 0.004 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 76 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8753 (ptp) cc_final: 0.8429 (ppp) REVERT: B 451 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7901 (ptm160) REVERT: D 313 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8374 (mpp) REVERT: F 142 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5621 (p) REVERT: F 313 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8732 (mmp) outliers start: 59 outliers final: 32 residues processed: 127 average time/residue: 1.4138 time to fit residues: 206.0773 Evaluate side-chains 111 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17014 Z= 0.219 Angle : 0.583 11.688 23087 Z= 0.293 Chirality : 0.050 0.637 2616 Planarity : 0.004 0.043 2949 Dihedral : 9.079 84.951 2482 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.40 % Allowed : 21.11 % Favored : 76.49 % 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: 0.47 (0.18), residues: 2104 helix: 2.93 (0.27), residues: 369 sheet: 1.20 (0.19), residues: 747 loop : -1.55 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 PHE 0.019 0.001 PHE B 126 TYR 0.011 0.001 TYR H 446 ARG 0.007 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7899 (ptm160) REVERT: D 85 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8006 (pmtt) REVERT: D 313 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (mpp) REVERT: F 142 THR cc_start: 0.5699 (OUTLIER) cc_final: 0.5385 (p) REVERT: F 313 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8716 (mmp) outliers start: 45 outliers final: 26 residues processed: 116 average time/residue: 1.4158 time to fit residues: 184.5225 Evaluate side-chains 105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 0.0470 chunk 114 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17014 Z= 0.166 Angle : 0.568 13.268 23087 Z= 0.283 Chirality : 0.049 0.608 2616 Planarity : 0.004 0.044 2949 Dihedral : 8.764 84.164 2482 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 21.75 % Favored : 76.33 % 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: 0.50 (0.18), residues: 2104 helix: 3.00 (0.27), residues: 371 sheet: 1.24 (0.19), residues: 738 loop : -1.54 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.001 0.000 HIS B 194 PHE 0.025 0.001 PHE H 126 TYR 0.010 0.001 TYR B 571 ARG 0.006 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 313 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8382 (mpp) REVERT: F 142 THR cc_start: 0.5697 (OUTLIER) cc_final: 0.5364 (p) outliers start: 36 outliers final: 24 residues processed: 108 average time/residue: 1.2835 time to fit residues: 156.9444 Evaluate side-chains 101 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 160 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17014 Z= 0.227 Angle : 0.581 13.745 23087 Z= 0.292 Chirality : 0.049 0.587 2616 Planarity : 0.004 0.044 2949 Dihedral : 8.548 83.668 2482 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.24 % Allowed : 21.27 % Favored : 76.49 % 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: 0.48 (0.18), residues: 2104 helix: 2.99 (0.27), residues: 369 sheet: 1.21 (0.19), residues: 739 loop : -1.54 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 461 HIS 0.002 0.000 HIS B 194 PHE 0.033 0.001 PHE D 403 TYR 0.012 0.001 TYR H 446 ARG 0.005 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 313 MET cc_start: 0.8659 (mmm) cc_final: 0.8331 (mpp) REVERT: D 313 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8404 (mpp) REVERT: F 142 THR cc_start: 0.5668 (OUTLIER) cc_final: 0.5328 (p) outliers start: 42 outliers final: 25 residues processed: 113 average time/residue: 1.2184 time to fit residues: 156.2341 Evaluate side-chains 101 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 492 THR Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 0.1980 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17014 Z= 0.177 Angle : 0.588 13.511 23087 Z= 0.292 Chirality : 0.049 0.572 2616 Planarity : 0.004 0.092 2949 Dihedral : 8.362 83.153 2479 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 22.01 % Favored : 76.23 % 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: 0.51 (0.18), residues: 2104 helix: 2.98 (0.26), residues: 370 sheet: 1.24 (0.19), residues: 729 loop : -1.49 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 461 HIS 0.001 0.000 HIS B 194 PHE 0.025 0.001 PHE B 126 TYR 0.010 0.001 TYR H 446 ARG 0.017 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 313 MET cc_start: 0.8631 (mmm) cc_final: 0.8318 (mpp) REVERT: B 501 MET cc_start: 0.9085 (mmt) cc_final: 0.8835 (mmt) REVERT: D 313 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (mpp) REVERT: F 142 THR cc_start: 0.5655 (OUTLIER) cc_final: 0.5313 (p) outliers start: 33 outliers final: 24 residues processed: 104 average time/residue: 1.2552 time to fit residues: 147.4635 Evaluate side-chains 99 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.7980 chunk 122 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 0.0470 chunk 168 optimal weight: 0.0030 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 17014 Z= 0.158 Angle : 0.587 13.360 23087 Z= 0.292 Chirality : 0.049 0.562 2616 Planarity : 0.004 0.077 2949 Dihedral : 8.205 82.596 2479 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.39 % Allowed : 22.17 % Favored : 76.44 % 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: 0.53 (0.18), residues: 2104 helix: 2.96 (0.27), residues: 370 sheet: 1.29 (0.19), residues: 717 loop : -1.45 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.001 0.000 HIS B 194 PHE 0.028 0.001 PHE B 126 TYR 0.014 0.001 TYR D 571 ARG 0.017 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 313 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8349 (mpp) REVERT: F 142 THR cc_start: 0.5623 (OUTLIER) cc_final: 0.5276 (p) outliers start: 26 outliers final: 18 residues processed: 98 average time/residue: 1.2757 time to fit residues: 141.8810 Evaluate side-chains 93 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 492 THR Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 0.0270 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.041815 restraints weight = 48573.586| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.54 r_work: 0.2540 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17014 Z= 0.172 Angle : 0.590 13.184 23087 Z= 0.292 Chirality : 0.049 0.553 2616 Planarity : 0.004 0.070 2949 Dihedral : 8.084 82.277 2478 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.28 % Allowed : 22.49 % Favored : 76.23 % 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: 0.55 (0.18), residues: 2104 helix: 2.94 (0.27), residues: 370 sheet: 1.35 (0.19), residues: 708 loop : -1.45 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 461 HIS 0.001 0.000 HIS B 194 PHE 0.028 0.001 PHE B 126 TYR 0.012 0.001 TYR D 571 ARG 0.016 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4700.58 seconds wall clock time: 86 minutes 37.71 seconds (5197.71 seconds total)