Starting phenix.real_space_refine on Sun Aug 24 03:31:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_36741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_36741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_36741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_36741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzb_36741/08_2025/8jzb_36741.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.97, per 1000 atoms: 0.24 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: 1.46 Conformation dependent library (CDL) restraints added in 766.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 3.24 Time building geometry restraints manager: 1.90 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: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- 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 17041 Z= 0.453 Angle : 1.051 20.410 23149 Z= 0.671 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 : 7.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG H 398 TYR 0.034 0.002 TYR B 446 PHE 0.017 0.002 PHE H 126 TRP 0.016 0.002 TRP D 461 HIS 0.006 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00650 (17014) covalent geometry : angle 1.01638 (23087) SS BOND : bond 0.00606 ( 19) SS BOND : angle 1.58329 ( 38) hydrogen bonds : bond 0.15080 ( 610) hydrogen bonds : angle 6.13917 ( 1710) link_BETA1-4 : bond 0.02548 ( 4) link_BETA1-4 : angle 7.98295 ( 12) link_NAG-ASN : bond 0.01224 ( 4) link_NAG-ASN : angle 8.37538 ( 12) *********************** 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 : 0.690 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: 0.6038 time to fit residues: 141.4895 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 : 0.645 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 ** 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 496 ASN H 591 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.040517 restraints weight = 48538.353| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.47 r_work: 0.2485 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17041 Z= 0.243 Angle : 0.716 16.977 23149 Z= 0.355 Chirality : 0.055 0.790 2616 Planarity : 0.004 0.053 2949 Dihedral : 12.490 87.184 2548 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.10 % Allowed : 20.79 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2104 helix: 2.83 (0.27), residues: 367 sheet: 1.30 (0.19), residues: 751 loop : -1.55 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 476 TYR 0.014 0.001 TYR B 571 PHE 0.040 0.002 PHE D 403 TRP 0.011 0.002 TRP D 274 HIS 0.002 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00574 (17014) covalent geometry : angle 0.66736 (23087) SS BOND : bond 0.00473 ( 19) SS BOND : angle 1.60399 ( 38) hydrogen bonds : bond 0.05701 ( 610) hydrogen bonds : angle 4.95749 ( 1710) link_BETA1-4 : bond 0.02897 ( 4) link_BETA1-4 : angle 6.68375 ( 12) link_NAG-ASN : bond 0.01213 ( 4) link_NAG-ASN : angle 8.92125 ( 12) *********************** 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 154 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 77 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8254 (ptm160) REVERT: D 313 MET cc_start: 0.8629 (mmm) cc_final: 0.8251 (mpp) outliers start: 77 outliers final: 36 residues processed: 145 average time/residue: 0.5601 time to fit residues: 92.1743 Evaluate side-chains 110 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 111 VAL Chi-restraints excluded: chain D residue 171 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 478 THR Chi-restraints excluded: chain D residue 492 THR 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 171 ASP Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain F residue 514 ILE 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 14 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 0.0070 chunk 158 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN D 71 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN F 71 GLN F 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.041008 restraints weight = 48720.706| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.56 r_work: 0.2507 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17041 Z= 0.143 Angle : 0.648 16.408 23149 Z= 0.313 Chirality : 0.052 0.731 2616 Planarity : 0.004 0.043 2949 Dihedral : 10.745 87.346 2499 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.09 % Allowed : 20.84 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2104 helix: 2.96 (0.27), residues: 368 sheet: 1.24 (0.19), residues: 753 loop : -1.50 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 476 TYR 0.013 0.001 TYR D 452 PHE 0.037 0.002 PHE D 403 TRP 0.010 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 Details of bonding type rmsd covalent geometry : bond 0.00313 (17014) covalent geometry : angle 0.59834 (23087) SS BOND : bond 0.00440 ( 19) SS BOND : angle 1.44724 ( 38) hydrogen bonds : bond 0.04883 ( 610) hydrogen bonds : angle 4.60996 ( 1710) link_BETA1-4 : bond 0.02865 ( 4) link_BETA1-4 : angle 6.40008 ( 12) link_NAG-ASN : bond 0.01226 ( 4) link_NAG-ASN : angle 8.58718 ( 12) *********************** 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 139 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 81 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8162 (ptm160) REVERT: D 134 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: D 313 MET cc_start: 0.8637 (mmm) cc_final: 0.8172 (mpp) REVERT: F 501 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7959 (mmm) REVERT: H 250 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8903 (p) outliers start: 58 outliers final: 21 residues processed: 132 average time/residue: 0.5739 time to fit residues: 85.3775 Evaluate side-chains 99 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 134 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS 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 501 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 171 ASP 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 497 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 18 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN D 71 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.041962 restraints weight = 48414.258| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.47 r_work: 0.2531 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17041 Z= 0.113 Angle : 0.617 16.282 23149 Z= 0.295 Chirality : 0.050 0.691 2616 Planarity : 0.004 0.038 2949 Dihedral : 9.599 86.443 2484 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.51 % Allowed : 21.43 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2104 helix: 2.91 (0.27), residues: 368 sheet: 1.27 (0.19), residues: 750 loop : -1.50 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 476 TYR 0.010 0.001 TYR B 571 PHE 0.034 0.001 PHE D 403 TRP 0.008 0.001 TRP D 274 HIS 0.001 0.000 HIS H 312 Details of bonding type rmsd covalent geometry : bond 0.00237 (17014) covalent geometry : angle 0.56610 (23087) SS BOND : bond 0.00367 ( 19) SS BOND : angle 1.41621 ( 38) hydrogen bonds : bond 0.04454 ( 610) hydrogen bonds : angle 4.42394 ( 1710) link_BETA1-4 : bond 0.02843 ( 4) link_BETA1-4 : angle 6.31065 ( 12) link_NAG-ASN : bond 0.01262 ( 4) link_NAG-ASN : angle 8.48937 ( 12) *********************** 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 124 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 77 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8421 (ptp) cc_final: 0.8029 (ppp) REVERT: B 451 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8257 (ptm160) REVERT: D 313 MET cc_start: 0.8657 (mmm) cc_final: 0.8169 (mpp) REVERT: D 372 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8080 (mmt90) REVERT: D 437 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8838 (p) REVERT: D 476 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8732 (mpp80) REVERT: F 142 THR cc_start: 0.4849 (OUTLIER) cc_final: 0.4631 (p) REVERT: F 313 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8208 (mmp) REVERT: F 501 MET cc_start: 0.8127 (mtt) cc_final: 0.7904 (mmm) REVERT: H 250 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8932 (p) outliers start: 47 outliers final: 21 residues processed: 117 average time/residue: 0.5682 time to fit residues: 75.2452 Evaluate side-chains 99 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 470 THR 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 240 LYS Chi-restraints excluded: chain D residue 372 ARG 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 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 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 409 LEU Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.040089 restraints weight = 48410.221| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.54 r_work: 0.2490 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17041 Z= 0.164 Angle : 0.625 16.140 23149 Z= 0.303 Chirality : 0.050 0.657 2616 Planarity : 0.004 0.043 2949 Dihedral : 9.266 85.454 2483 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.25 % Allowed : 20.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2104 helix: 2.91 (0.27), residues: 369 sheet: 1.22 (0.19), residues: 746 loop : -1.50 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.013 0.001 TYR H 446 PHE 0.018 0.001 PHE B 126 TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00382 (17014) covalent geometry : angle 0.57540 (23087) SS BOND : bond 0.00351 ( 19) SS BOND : angle 1.59012 ( 38) hydrogen bonds : bond 0.04729 ( 610) hydrogen bonds : angle 4.44779 ( 1710) link_BETA1-4 : bond 0.02749 ( 4) link_BETA1-4 : angle 6.19979 ( 12) link_NAG-ASN : bond 0.01238 ( 4) link_NAG-ASN : angle 8.37290 ( 12) *********************** 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 137 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 76 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8555 (ptp) cc_final: 0.8152 (ppp) REVERT: B 451 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8318 (ptm160) REVERT: B 603 MET cc_start: 0.8512 (mtt) cc_final: 0.8119 (mtt) REVERT: D 85 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8105 (pmtt) REVERT: D 313 MET cc_start: 0.8868 (mmm) cc_final: 0.8536 (mmm) REVERT: D 372 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (mmt90) REVERT: F 142 THR cc_start: 0.4843 (OUTLIER) cc_final: 0.4578 (p) REVERT: F 313 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8537 (mmp) REVERT: F 501 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8216 (mmm) REVERT: H 250 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9163 (p) outliers start: 61 outliers final: 28 residues processed: 129 average time/residue: 0.5576 time to fit residues: 81.5623 Evaluate side-chains 110 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 85 LYS Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 372 ARG 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 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 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 501 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 250 SER 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 28 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.040144 restraints weight = 48181.910| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.46 r_work: 0.2491 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17041 Z= 0.172 Angle : 0.637 16.076 23149 Z= 0.307 Chirality : 0.050 0.636 2616 Planarity : 0.004 0.040 2949 Dihedral : 9.069 84.860 2482 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.04 % Allowed : 20.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2104 helix: 2.91 (0.27), residues: 370 sheet: 1.18 (0.19), residues: 743 loop : -1.52 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.012 0.001 TYR B 446 PHE 0.022 0.001 PHE D 403 TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00402 (17014) covalent geometry : angle 0.58928 (23087) SS BOND : bond 0.00434 ( 19) SS BOND : angle 1.52936 ( 38) hydrogen bonds : bond 0.04713 ( 610) hydrogen bonds : angle 4.43024 ( 1710) link_BETA1-4 : bond 0.02730 ( 4) link_BETA1-4 : angle 6.15067 ( 12) link_NAG-ASN : bond 0.01237 ( 4) link_NAG-ASN : angle 8.32361 ( 12) *********************** 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 135 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 78 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8550 (ptp) cc_final: 0.8145 (ppp) REVERT: B 451 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8389 (ptm160) REVERT: B 603 MET cc_start: 0.8539 (mtt) cc_final: 0.8177 (mtt) REVERT: D 134 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8746 (tp30) REVERT: D 313 MET cc_start: 0.8860 (mmm) cc_final: 0.8495 (mmm) REVERT: D 372 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8087 (mmt90) REVERT: D 403 PHE cc_start: 0.7747 (p90) cc_final: 0.7543 (p90) REVERT: F 74 MET cc_start: 0.7993 (ttp) cc_final: 0.7767 (ptm) REVERT: F 142 THR cc_start: 0.4893 (OUTLIER) cc_final: 0.4619 (p) REVERT: F 313 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8521 (mmp) REVERT: F 501 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (mmm) REVERT: H 135 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9103 (tm-30) REVERT: H 250 SER cc_start: 0.9414 (OUTLIER) cc_final: 0.9213 (p) REVERT: H 483 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8115 (mp0) outliers start: 57 outliers final: 28 residues processed: 124 average time/residue: 0.6009 time to fit residues: 83.5496 Evaluate side-chains 111 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 243 CYS 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 134 GLU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 372 ARG 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 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 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 501 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 135 GLU 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 250 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 483 GLU 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 88 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.040134 restraints weight = 48023.384| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.44 r_work: 0.2495 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17041 Z= 0.157 Angle : 0.634 16.164 23149 Z= 0.305 Chirality : 0.050 0.612 2616 Planarity : 0.004 0.041 2949 Dihedral : 8.842 84.332 2482 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.40 % Allowed : 21.22 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2104 helix: 2.94 (0.27), residues: 370 sheet: 1.17 (0.19), residues: 739 loop : -1.52 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.011 0.001 TYR H 446 PHE 0.025 0.001 PHE H 126 TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00363 (17014) covalent geometry : angle 0.58729 (23087) SS BOND : bond 0.00426 ( 19) SS BOND : angle 1.43203 ( 38) hydrogen bonds : bond 0.04620 ( 610) hydrogen bonds : angle 4.39315 ( 1710) link_BETA1-4 : bond 0.02761 ( 4) link_BETA1-4 : angle 6.14205 ( 12) link_NAG-ASN : bond 0.01224 ( 4) link_NAG-ASN : angle 8.26038 ( 12) *********************** 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 124 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8566 (ptp) cc_final: 0.8216 (ppp) REVERT: B 401 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8286 (mmm) REVERT: B 603 MET cc_start: 0.8558 (mtt) cc_final: 0.8182 (mtt) REVERT: D 85 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7823 (pmtt) REVERT: D 134 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8754 (tp30) REVERT: D 313 MET cc_start: 0.8881 (mmm) cc_final: 0.8493 (mmm) REVERT: D 372 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8014 (mmt90) REVERT: F 142 THR cc_start: 0.4892 (OUTLIER) cc_final: 0.4612 (p) REVERT: F 313 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8577 (mmp) REVERT: F 501 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: H 135 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9081 (tm-30) REVERT: H 401 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8189 (mpp) outliers start: 45 outliers final: 26 residues processed: 117 average time/residue: 0.5892 time to fit residues: 77.6511 Evaluate side-chains 109 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 243 CYS 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 565 THR 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 134 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 372 ARG 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 501 MET Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 135 GLU 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 401 MET 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 6 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 371 ASN D 64 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.039918 restraints weight = 48743.728| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.54 r_work: 0.2483 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17041 Z= 0.183 Angle : 0.647 15.987 23149 Z= 0.316 Chirality : 0.050 0.588 2616 Planarity : 0.004 0.045 2949 Dihedral : 8.633 83.989 2480 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.61 % Allowed : 21.11 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2104 helix: 2.88 (0.26), residues: 370 sheet: 1.07 (0.18), residues: 750 loop : -1.54 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 451 TYR 0.013 0.001 TYR B 446 PHE 0.034 0.002 PHE D 403 TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00432 (17014) covalent geometry : angle 0.60203 (23087) SS BOND : bond 0.00430 ( 19) SS BOND : angle 1.48287 ( 38) hydrogen bonds : bond 0.04769 ( 610) hydrogen bonds : angle 4.46658 ( 1710) link_BETA1-4 : bond 0.02668 ( 4) link_BETA1-4 : angle 6.06353 ( 12) link_NAG-ASN : bond 0.01203 ( 4) link_NAG-ASN : angle 8.21307 ( 12) *********************** 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 125 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 76 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8575 (ptp) cc_final: 0.8198 (ppp) REVERT: B 371 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8287 (p0) REVERT: B 372 ARG cc_start: 0.9443 (mtt180) cc_final: 0.9157 (mmm160) REVERT: B 401 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7843 (mmm) REVERT: B 603 MET cc_start: 0.8436 (mtt) cc_final: 0.8059 (mtt) REVERT: D 313 MET cc_start: 0.8814 (mmm) cc_final: 0.8490 (mmm) REVERT: D 372 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8017 (mmt90) REVERT: D 572 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8945 (mptm) REVERT: F 88 MET cc_start: 0.8615 (ptm) cc_final: 0.8350 (ttp) REVERT: F 142 THR cc_start: 0.4680 (OUTLIER) cc_final: 0.4426 (p) REVERT: F 313 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8377 (mmp) REVERT: H 135 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.9062 (tm-30) REVERT: H 401 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7966 (mpp) outliers start: 49 outliers final: 31 residues processed: 117 average time/residue: 0.5670 time to fit residues: 75.0561 Evaluate side-chains 112 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 243 CYS Chi-restraints excluded: chain B residue 371 ASN 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 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 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 372 ARG 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 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 572 LYS 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 H residue 93 ASP Chi-restraints excluded: chain H residue 135 GLU 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 401 MET Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 146 optimal weight: 0.0040 chunk 26 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.060340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.040928 restraints weight = 48420.648| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.53 r_work: 0.2514 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17041 Z= 0.116 Angle : 0.634 16.051 23149 Z= 0.303 Chirality : 0.049 0.574 2616 Planarity : 0.004 0.047 2949 Dihedral : 8.445 83.374 2480 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.87 % Allowed : 21.75 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2104 helix: 2.98 (0.27), residues: 369 sheet: 1.21 (0.19), residues: 737 loop : -1.49 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 372 TYR 0.010 0.001 TYR B 571 PHE 0.025 0.001 PHE F 89 TRP 0.009 0.001 TRP D 461 HIS 0.001 0.000 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00249 (17014) covalent geometry : angle 0.58688 (23087) SS BOND : bond 0.00400 ( 19) SS BOND : angle 1.74890 ( 38) hydrogen bonds : bond 0.04333 ( 610) hydrogen bonds : angle 4.33850 ( 1710) link_BETA1-4 : bond 0.02715 ( 4) link_BETA1-4 : angle 6.08741 ( 12) link_NAG-ASN : bond 0.01223 ( 4) link_NAG-ASN : angle 8.13848 ( 12) *********************** 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 110 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8550 (ptp) cc_final: 0.8192 (ppp) REVERT: B 313 MET cc_start: 0.8129 (mmm) cc_final: 0.7512 (mpp) REVERT: B 372 ARG cc_start: 0.9398 (mtt180) cc_final: 0.9173 (mmm160) REVERT: B 401 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7934 (mmm) REVERT: B 603 MET cc_start: 0.8499 (mtt) cc_final: 0.8036 (mtt) REVERT: D 313 MET cc_start: 0.8768 (mmm) cc_final: 0.8378 (mmm) REVERT: F 142 THR cc_start: 0.4619 (OUTLIER) cc_final: 0.4350 (p) REVERT: F 313 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8338 (mmp) REVERT: H 135 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.9045 (tm-30) REVERT: H 401 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7955 (mpp) outliers start: 35 outliers final: 21 residues processed: 106 average time/residue: 0.5877 time to fit residues: 70.4639 Evaluate side-chains 97 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 243 CYS 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 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 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 H residue 78 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 401 MET 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 68 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 153 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN B 548 HIS ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.039323 restraints weight = 49000.328| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.53 r_work: 0.2464 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17041 Z= 0.254 Angle : 0.690 15.948 23149 Z= 0.340 Chirality : 0.051 0.557 2616 Planarity : 0.004 0.051 2949 Dihedral : 8.462 83.921 2480 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.87 % Allowed : 22.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2104 helix: 2.75 (0.27), residues: 368 sheet: 1.07 (0.19), residues: 749 loop : -1.52 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 451 TYR 0.017 0.001 TYR B 446 PHE 0.030 0.002 PHE D 403 TRP 0.010 0.001 TRP F 576 HIS 0.002 0.001 HIS F 381 Details of bonding type rmsd covalent geometry : bond 0.00611 (17014) covalent geometry : angle 0.64697 (23087) SS BOND : bond 0.00468 ( 19) SS BOND : angle 1.82232 ( 38) hydrogen bonds : bond 0.05137 ( 610) hydrogen bonds : angle 4.56497 ( 1710) link_BETA1-4 : bond 0.02653 ( 4) link_BETA1-4 : angle 5.97580 ( 12) link_NAG-ASN : bond 0.01127 ( 4) link_NAG-ASN : angle 8.10429 ( 12) ********************** 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 109 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8563 (ptp) cc_final: 0.8195 (ppp) REVERT: B 371 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8244 (p0) REVERT: B 372 ARG cc_start: 0.9433 (mtt180) cc_final: 0.9171 (mmm160) REVERT: B 401 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7751 (mmm) REVERT: B 603 MET cc_start: 0.8405 (mtt) cc_final: 0.7989 (mtt) REVERT: D 313 MET cc_start: 0.8888 (mmm) cc_final: 0.8560 (mmm) REVERT: D 572 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8972 (mptm) REVERT: F 142 THR cc_start: 0.4700 (OUTLIER) cc_final: 0.4446 (p) REVERT: F 313 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8402 (mmp) REVERT: H 135 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.9066 (tm-30) REVERT: H 401 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7930 (mpp) outliers start: 35 outliers final: 19 residues processed: 104 average time/residue: 0.5754 time to fit residues: 67.9758 Evaluate side-chains 98 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 243 CYS Chi-restraints excluded: chain B residue 371 ASN 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 565 THR Chi-restraints excluded: chain D residue 240 LYS 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 D residue 572 LYS Chi-restraints excluded: chain F residue 142 THR 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 H residue 135 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 401 MET Chi-restraints excluded: chain H residue 470 THR 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 109 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 102 optimal weight: 0.0070 chunk 118 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.039420 restraints weight = 48509.952| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 3.51 r_work: 0.2468 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.230 17041 Z= 0.278 Angle : 0.873 59.180 23149 Z= 0.484 Chirality : 0.051 0.556 2616 Planarity : 0.004 0.050 2949 Dihedral : 8.447 83.887 2479 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.65 % Allowed : 22.33 % Favored : 76.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.18), residues: 2104 helix: 2.75 (0.27), residues: 368 sheet: 1.06 (0.19), residues: 749 loop : -1.52 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.016 0.001 TYR B 446 PHE 0.022 0.002 PHE B 126 TRP 0.010 0.001 TRP F 576 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00600 (17014) covalent geometry : angle 0.83986 (23087) SS BOND : bond 0.00419 ( 19) SS BOND : angle 1.75006 ( 38) hydrogen bonds : bond 0.05026 ( 610) hydrogen bonds : angle 4.56955 ( 1710) link_BETA1-4 : bond 0.02917 ( 4) link_BETA1-4 : angle 6.19825 ( 12) link_NAG-ASN : bond 0.01119 ( 4) link_NAG-ASN : angle 8.10222 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.04 seconds wall clock time: 86 minutes 18.80 seconds (5178.80 seconds total)