Starting phenix.real_space_refine on Sun May 18 07:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzb_36741/05_2025/8jzb_36741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzb_36741/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzb_36741/05_2025/8jzb_36741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzb_36741/05_2025/8jzb_36741.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzb_36741/05_2025/8jzb_36741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzb_36741/05_2025/8jzb_36741.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 Na 6 4.78 5 C 10548 2.51 5 N 2713 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "D" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "F" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "H" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.30, per 1000 atoms: 0.62 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 25 sheets defined 19.4% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.517A pdb=" N LEU B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.758A pdb=" N VAL B 400 " --> pdb=" O CYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.791A pdb=" N THR B 478 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 99 removed outlier: 3.532A pdb=" N VAL D 82 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'F' and resid 62 through 99 removed outlier: 3.725A pdb=" N THR F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 73 " --> pdb=" O LYS F 69 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 113 through 141 Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 391 through 400 removed outlier: 3.718A pdb=" N VAL F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 437 removed outlier: 3.769A pdb=" N SER F 437 " --> pdb=" O PRO F 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 99 removed outlier: 4.648A pdb=" N LYS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 113 through 141 Processing helix chain 'H' and resid 162 through 169 removed outlier: 3.599A pdb=" N ASP H 166 " --> pdb=" O LYS H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 391 through 400 removed outlier: 3.782A pdb=" N VAL H 400 " --> pdb=" O CYS H 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 177 through 178 current: chain 'B' and resid 560 through 571 removed outlier: 5.531A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 218 through 227 removed outlier: 6.521A pdb=" N SER B 235 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 225 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET B 233 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE B 227 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 248 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 251 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER B 275 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 253 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 273 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 255 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 282 through 290 removed outlier: 3.751A pdb=" N SER B 284 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 339 current: chain 'B' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 360 through 370 current: chain 'B' and resid 405 through 418 Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 448 removed outlier: 4.238A pdb=" N ARG B 466 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 515 through 516 removed outlier: 4.529A pdb=" N SER B 538 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 193 through 199 current: chain 'D' and resid 574 through 584 removed outlier: 4.336A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 227 removed outlier: 6.338A pdb=" N SER D 235 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE D 225 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET D 233 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE D 227 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS D 240 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE D 248 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE D 251 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER D 275 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE D 253 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL D 273 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 255 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.617A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 316 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 339 current: chain 'D' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 360 through 370 current: chain 'D' and resid 405 through 418 Processing sheet with id=AB2, first strand: chain 'D' and resid 443 through 448 Processing sheet with id=AB3, first strand: chain 'D' and resid 514 through 516 removed outlier: 4.545A pdb=" N SER D 538 " --> pdb=" O ILE D 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 177 through 178 current: chain 'F' and resid 560 through 571 removed outlier: 5.526A pdb=" N ILE F 561 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG F 584 " --> pdb=" O ILE F 561 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER F 563 " --> pdb=" O GLU F 582 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU F 582 " --> pdb=" O SER F 563 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 575 " --> pdb=" O VAL F 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 218 through 227 removed outlier: 6.532A pdb=" N SER F 235 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE F 225 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET F 233 " --> pdb=" O PHE F 225 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE F 227 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 231 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER F 250 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS F 240 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 248 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE F 251 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER F 275 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE F 253 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 273 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 255 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 282 through 289 removed outlier: 6.640A pdb=" N SER F 299 " --> pdb=" O ASN F 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS F 285 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 297 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL F 287 " --> pdb=" O TRP F 295 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 295 " --> pdb=" O VAL F 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 338 through 339 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 339 current: chain 'F' and resid 360 through 369 Processing sheet with id=AB8, first strand: chain 'F' and resid 401 through 402 removed outlier: 5.737A pdb=" N SER F 408 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 443 through 448 Processing sheet with id=AC1, first strand: chain 'F' and resid 514 through 516 removed outlier: 4.338A pdb=" N SER F 538 " --> pdb=" O ILE F 554 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 575 through 584 removed outlier: 4.289A pdb=" N ILE H 575 " --> pdb=" O VAL H 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 218 through 227 removed outlier: 6.514A pdb=" N SER H 235 " --> pdb=" O PRO H 223 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE H 225 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET H 233 " --> pdb=" O PHE H 225 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE H 227 " --> pdb=" O ILE H 231 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE H 231 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR H 232 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU H 255 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE H 234 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE H 253 " --> pdb=" O PHE H 234 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN H 236 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE H 251 " --> pdb=" O GLN H 236 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE H 238 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 257 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL H 259 " --> pdb=" O ALA H 268 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA H 268 " --> pdb=" O VAL H 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 282 through 289 removed outlier: 4.169A pdb=" N SER H 284 " --> pdb=" O SER H 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 338 through 340 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 338 through 340 current: chain 'H' and resid 360 through 370 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 360 through 370 current: chain 'H' and resid 405 through 418 Processing sheet with id=AC6, first strand: chain 'H' and resid 443 through 448 removed outlier: 4.212A pdb=" N ARG H 466 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N SER H 477 " --> pdb=" O PRO H 471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 515 through 516 removed outlier: 4.275A pdb=" N SER H 538 " --> pdb=" O ILE H 554 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 4.70 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.290 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.400 ------------------------------------------------------------------------------- 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 : 6.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.14 % Favored : 97.72 % Rotamer: Outliers : 6.93 % Allowed : 19.40 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 364 sheet: 1.34 (0.19), residues: 754 loop : -1.47 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 461 HIS 0.006 0.001 HIS B 596 PHE 0.017 0.002 PHE H 126 TYR 0.034 0.002 TYR B 446 ARG 0.005 0.000 ARG H 398 Details of bonding type rmsd link_NAG-ASN : bond 0.01224 ( 4) link_NAG-ASN : angle 8.37538 ( 12) link_BETA1-4 : bond 0.02548 ( 4) link_BETA1-4 : angle 7.98295 ( 12) hydrogen bonds : bond 0.15080 ( 610) hydrogen bonds : angle 6.13917 ( 1710) SS BOND : bond 0.00606 ( 19) SS BOND : angle 1.58329 ( 38) covalent geometry : bond 0.00650 (17014) covalent geometry : angle 1.01638 (23087) *********************** 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 : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8869 (m) REVERT: B 359 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 603 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7826 (mtt) REVERT: D 83 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7044 (p0) REVERT: D 501 MET cc_start: 0.9042 (mmt) cc_final: 0.8327 (mmm) REVERT: F 460 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8775 (p) REVERT: H 78 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7936 (mp) outliers start: 130 outliers final: 40 residues processed: 210 average time/residue: 1.1304 time to fit residues: 267.5271 Evaluate side-chains 123 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN B 359 ASN B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 263 GLN D 430 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN F 430 GLN H 64 ASN H 70 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 591 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.040831 restraints weight = 48490.643| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.54 r_work: 0.2498 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17041 Z= 0.209 Angle : 0.705 16.916 23149 Z= 0.346 Chirality : 0.055 0.785 2616 Planarity : 0.004 0.051 2949 Dihedral : 12.292 86.537 2548 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.05 % Allowed : 20.90 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2104 helix: 2.82 (0.27), residues: 367 sheet: 1.29 (0.19), residues: 753 loop : -1.52 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.002 0.001 HIS B 194 PHE 0.041 0.002 PHE D 403 TYR 0.014 0.001 TYR B 571 ARG 0.006 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 4) link_NAG-ASN : angle 8.93151 ( 12) link_BETA1-4 : bond 0.02892 ( 4) link_BETA1-4 : angle 6.63226 ( 12) hydrogen bonds : bond 0.05468 ( 610) hydrogen bonds : angle 4.89539 ( 1710) SS BOND : bond 0.00446 ( 19) SS BOND : angle 1.55868 ( 38) covalent geometry : bond 0.00488 (17014) covalent geometry : angle 0.65586 (23087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 77 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8245 (ptm160) REVERT: B 603 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7446 (mtt) REVERT: D 313 MET cc_start: 0.8598 (mmm) cc_final: 0.8226 (mpp) REVERT: D 501 MET cc_start: 0.8853 (mmt) cc_final: 0.7844 (mmm) REVERT: F 501 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7837 (mmm) outliers start: 76 outliers final: 30 residues processed: 144 average time/residue: 1.1366 time to fit residues: 187.0258 Evaluate side-chains 108 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 501 MET Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 105 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN F 71 GLN F 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.041662 restraints weight = 48158.426| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.54 r_work: 0.2526 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17041 Z= 0.122 Angle : 0.641 16.400 23149 Z= 0.308 Chirality : 0.051 0.727 2616 Planarity : 0.004 0.043 2949 Dihedral : 10.621 87.303 2495 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.83 % Allowed : 21.06 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2104 helix: 2.98 (0.27), residues: 368 sheet: 1.29 (0.19), residues: 753 loop : -1.48 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 PHE 0.032 0.001 PHE D 403 TYR 0.014 0.001 TYR D 452 ARG 0.008 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.01248 ( 4) link_NAG-ASN : angle 8.56253 ( 12) link_BETA1-4 : bond 0.02873 ( 4) link_BETA1-4 : angle 6.40882 ( 12) hydrogen bonds : bond 0.04731 ( 610) hydrogen bonds : angle 4.58172 ( 1710) SS BOND : bond 0.00367 ( 19) SS BOND : angle 1.39828 ( 38) covalent geometry : bond 0.00258 (17014) covalent geometry : angle 0.59148 (23087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 82 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8221 (ptm160) REVERT: D 134 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8661 (tp30) REVERT: D 313 MET cc_start: 0.8591 (mmm) cc_final: 0.8142 (mpp) REVERT: F 501 MET cc_start: 0.8046 (mtt) cc_final: 0.7818 (mmm) outliers start: 53 outliers final: 24 residues processed: 127 average time/residue: 1.1047 time to fit residues: 159.5927 Evaluate side-chains 100 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 115 optimal weight: 4.9990 chunk 185 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 chunk 177 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3154 r_free = 0.3154 target = 0.060214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.040740 restraints weight = 48211.671| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.52 r_work: 0.2504 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1667 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 : 0.636 16.405 23149 Z= 0.307 Chirality : 0.051 0.702 2616 Planarity : 0.004 0.038 2949 Dihedral : 9.715 86.665 2484 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.14 % Allowed : 20.52 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 368 sheet: 1.25 (0.18), residues: 758 loop : -1.53 (0.17), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 PHE 0.032 0.001 PHE D 403 TYR 0.013 0.001 TYR H 446 ARG 0.002 0.000 ARG B 451 Details of bonding type rmsd link_NAG-ASN : bond 0.01244 ( 4) link_NAG-ASN : angle 8.51934 ( 12) link_BETA1-4 : bond 0.02804 ( 4) link_BETA1-4 : angle 6.31195 ( 12) hydrogen bonds : bond 0.04791 ( 610) hydrogen bonds : angle 4.51725 ( 1710) SS BOND : bond 0.00376 ( 19) SS BOND : angle 1.46938 ( 38) covalent geometry : bond 0.00378 (17014) covalent geometry : angle 0.58601 (23087) *********************** 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 135 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 76 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8252 (ptm160) REVERT: B 603 MET cc_start: 0.8307 (mtt) cc_final: 0.8056 (mtt) REVERT: D 313 MET cc_start: 0.8721 (mmm) cc_final: 0.8229 (mpp) REVERT: D 372 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (mmt90) REVERT: F 142 THR cc_start: 0.4840 (OUTLIER) cc_final: 0.4627 (p) REVERT: F 313 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8243 (mmp) REVERT: F 501 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7908 (mmm) REVERT: H 250 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.8928 (p) outliers start: 59 outliers final: 25 residues processed: 128 average time/residue: 1.0708 time to fit residues: 157.0503 Evaluate side-chains 104 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 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 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 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 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 F residue 502 CYS Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 492 THR Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 430 GLN ** H 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 = 0.3162 r_free = 0.3162 target = 0.060415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.040917 restraints weight = 48714.116| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.55 r_work: 0.2509 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17041 Z= 0.140 Angle : 0.618 16.228 23149 Z= 0.297 Chirality : 0.050 0.662 2616 Planarity : 0.004 0.040 2949 Dihedral : 9.288 85.604 2483 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.51 % Allowed : 20.95 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2104 helix: 2.96 (0.27), residues: 368 sheet: 1.23 (0.19), residues: 748 loop : -1.53 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 PHE 0.016 0.001 PHE B 126 TYR 0.012 0.001 TYR H 446 ARG 0.005 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.01252 ( 4) link_NAG-ASN : angle 8.38461 ( 12) link_BETA1-4 : bond 0.02786 ( 4) link_BETA1-4 : angle 6.23103 ( 12) hydrogen bonds : bond 0.04588 ( 610) hydrogen bonds : angle 4.42728 ( 1710) SS BOND : bond 0.00349 ( 19) SS BOND : angle 1.56685 ( 38) covalent geometry : bond 0.00317 (17014) covalent geometry : angle 0.56774 (23087) *********************** 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 122 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8484 (ttm) cc_final: 0.8237 (ppp) REVERT: B 451 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8214 (ptm160) REVERT: D 134 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8643 (tp30) REVERT: D 308 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8767 (tp30) REVERT: D 313 MET cc_start: 0.8763 (mmm) cc_final: 0.8430 (mmm) REVERT: D 372 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8060 (mmt90) REVERT: F 142 THR cc_start: 0.4825 (OUTLIER) cc_final: 0.4599 (p) REVERT: F 313 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8278 (mmp) REVERT: H 250 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8967 (p) outliers start: 47 outliers final: 23 residues processed: 117 average time/residue: 1.2793 time to fit residues: 170.5181 Evaluate side-chains 103 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 484 LYS 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 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 11 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.040908 restraints weight = 48514.794| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.54 r_work: 0.2511 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17041 Z= 0.134 Angle : 0.618 16.162 23149 Z= 0.296 Chirality : 0.050 0.639 2616 Planarity : 0.003 0.038 2949 Dihedral : 9.043 84.926 2482 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.77 % Allowed : 21.00 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2104 helix: 3.01 (0.27), residues: 369 sheet: 1.22 (0.18), residues: 748 loop : -1.50 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 PHE 0.023 0.001 PHE H 126 TYR 0.011 0.001 TYR H 446 ARG 0.008 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.01252 ( 4) link_NAG-ASN : angle 8.31723 ( 12) link_BETA1-4 : bond 0.02743 ( 4) link_BETA1-4 : angle 6.18724 ( 12) hydrogen bonds : bond 0.04454 ( 610) hydrogen bonds : angle 4.37254 ( 1710) SS BOND : bond 0.00307 ( 19) SS BOND : angle 1.46770 ( 38) covalent geometry : bond 0.00303 (17014) covalent geometry : angle 0.56926 (23087) *********************** 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 129 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 77 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8499 (ttm) cc_final: 0.8262 (ppp) REVERT: B 451 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (ptm160) REVERT: D 85 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7755 (pmtt) REVERT: D 313 MET cc_start: 0.8709 (mmm) cc_final: 0.8343 (mmm) REVERT: D 372 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8076 (mmt90) REVERT: D 403 PHE cc_start: 0.7582 (p90) cc_final: 0.7339 (p90) REVERT: D 534 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 572 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8870 (mptm) REVERT: F 142 THR cc_start: 0.4591 (OUTLIER) cc_final: 0.4334 (p) REVERT: F 313 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8422 (mmp) REVERT: H 250 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.9006 (p) outliers start: 52 outliers final: 29 residues processed: 120 average time/residue: 1.1601 time to fit residues: 158.2318 Evaluate side-chains 109 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 111 VAL 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 441 SER 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 F residue 502 CYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3140 r_free = 0.3140 target = 0.059437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.039912 restraints weight = 48616.178| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.54 r_work: 0.2484 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17041 Z= 0.186 Angle : 0.632 16.032 23149 Z= 0.306 Chirality : 0.050 0.609 2616 Planarity : 0.004 0.041 2949 Dihedral : 8.821 84.247 2482 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2104 helix: 3.03 (0.27), residues: 370 sheet: 1.16 (0.19), residues: 743 loop : -1.54 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 PHE 0.021 0.002 PHE B 126 TYR 0.014 0.001 TYR B 446 ARG 0.003 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.01207 ( 4) link_NAG-ASN : angle 8.25004 ( 12) link_BETA1-4 : bond 0.02684 ( 4) link_BETA1-4 : angle 6.09986 ( 12) hydrogen bonds : bond 0.04794 ( 610) hydrogen bonds : angle 4.44361 ( 1710) SS BOND : bond 0.00329 ( 19) SS BOND : angle 1.38346 ( 38) covalent geometry : bond 0.00437 (17014) covalent geometry : angle 0.58488 (23087) *********************** 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 129 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 372 ARG cc_start: 0.9429 (mtt180) cc_final: 0.9048 (mmm160) REVERT: B 603 MET cc_start: 0.8501 (mtt) cc_final: 0.8202 (mtt) REVERT: D 313 MET cc_start: 0.8789 (mmm) cc_final: 0.8472 (mmm) REVERT: D 476 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8814 (mpp80) REVERT: D 534 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 572 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8926 (mptm) REVERT: F 142 THR cc_start: 0.4609 (OUTLIER) cc_final: 0.4350 (p) REVERT: F 313 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8380 (mmp) REVERT: H 135 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.9017 (tm-30) REVERT: H 250 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9066 (p) outliers start: 49 outliers final: 28 residues processed: 124 average time/residue: 1.0751 time to fit residues: 152.2402 Evaluate side-chains 106 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 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 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 F residue 502 CYS 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 250 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3158 r_free = 0.3158 target = 0.060131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.040693 restraints weight = 48463.070| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.53 r_work: 0.2505 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17041 Z= 0.129 Angle : 0.622 15.965 23149 Z= 0.298 Chirality : 0.049 0.587 2616 Planarity : 0.003 0.044 2949 Dihedral : 8.556 83.688 2480 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.24 % Allowed : 21.32 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2104 helix: 2.96 (0.26), residues: 372 sheet: 1.19 (0.19), residues: 739 loop : -1.55 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.001 0.000 HIS B 194 PHE 0.035 0.001 PHE D 403 TYR 0.011 0.001 TYR H 446 ARG 0.004 0.000 ARG B 451 Details of bonding type rmsd link_NAG-ASN : bond 0.01234 ( 4) link_NAG-ASN : angle 8.19047 ( 12) link_BETA1-4 : bond 0.02667 ( 4) link_BETA1-4 : angle 6.08439 ( 12) hydrogen bonds : bond 0.04382 ( 610) hydrogen bonds : angle 4.37253 ( 1710) SS BOND : bond 0.00483 ( 19) SS BOND : angle 1.65200 ( 38) covalent geometry : bond 0.00292 (17014) covalent geometry : angle 0.57353 (23087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8142 (ptm) REVERT: B 313 MET cc_start: 0.8134 (mmm) cc_final: 0.7512 (mpp) REVERT: B 372 ARG cc_start: 0.9429 (mtt180) cc_final: 0.9049 (mmm160) REVERT: B 501 MET cc_start: 0.8869 (mmt) cc_final: 0.8473 (mmt) REVERT: B 603 MET cc_start: 0.8545 (mtt) cc_final: 0.8185 (mtt) REVERT: D 313 MET cc_start: 0.8769 (mmm) cc_final: 0.8450 (mmm) REVERT: D 476 ARG cc_start: 0.9132 (mmm-85) cc_final: 0.8869 (mpp80) REVERT: D 572 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8895 (mptm) REVERT: F 88 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (ttp) REVERT: F 142 THR cc_start: 0.4604 (OUTLIER) cc_final: 0.4338 (p) REVERT: F 313 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8482 (mmp) REVERT: H 74 MET cc_start: 0.8807 (mpp) cc_final: 0.8445 (ptp) REVERT: H 135 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.9043 (tm-30) REVERT: H 250 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.9065 (p) outliers start: 42 outliers final: 30 residues processed: 113 average time/residue: 1.1808 time to fit residues: 151.2393 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 : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE 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 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 538 SER 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 88 MET Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 71 GLN 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 250 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 485 ASP 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 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3161 r_free = 0.3161 target = 0.060347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.040926 restraints weight = 48341.459| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.54 r_work: 0.2513 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17041 Z= 0.122 Angle : 0.631 15.947 23149 Z= 0.302 Chirality : 0.049 0.574 2616 Planarity : 0.004 0.044 2949 Dihedral : 8.397 83.315 2480 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 21.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2104 helix: 3.01 (0.26), residues: 370 sheet: 1.22 (0.19), residues: 737 loop : -1.52 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.001 0.000 HIS B 194 PHE 0.024 0.001 PHE B 126 TYR 0.010 0.001 TYR H 446 ARG 0.004 0.000 ARG B 451 Details of bonding type rmsd link_NAG-ASN : bond 0.01231 ( 4) link_NAG-ASN : angle 8.13268 ( 12) link_BETA1-4 : bond 0.02678 ( 4) link_BETA1-4 : angle 6.06805 ( 12) hydrogen bonds : bond 0.04266 ( 610) hydrogen bonds : angle 4.31873 ( 1710) SS BOND : bond 0.00410 ( 19) SS BOND : angle 1.48771 ( 38) covalent geometry : bond 0.00273 (17014) covalent geometry : angle 0.58473 (23087) *********************** 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 112 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8153 (ptm) REVERT: B 313 MET cc_start: 0.8124 (mmm) cc_final: 0.7507 (mpp) REVERT: B 372 ARG cc_start: 0.9405 (mtt180) cc_final: 0.9043 (mmm160) REVERT: B 401 MET cc_start: 0.8530 (tpp) cc_final: 0.8112 (mmm) REVERT: B 603 MET cc_start: 0.8568 (mtt) cc_final: 0.8200 (mtt) REVERT: D 313 MET cc_start: 0.8754 (mmm) cc_final: 0.8453 (mmm) REVERT: D 372 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7997 (mmt90) REVERT: D 476 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8894 (mpp80) REVERT: D 572 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8882 (mptm) REVERT: F 142 THR cc_start: 0.4566 (OUTLIER) cc_final: 0.4303 (p) REVERT: H 135 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9036 (tm-30) REVERT: H 250 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9087 (p) outliers start: 37 outliers final: 26 residues processed: 108 average time/residue: 1.1903 time to fit residues: 146.9527 Evaluate side-chains 105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 171 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 538 SER 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 293 THR Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 71 GLN 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 250 SER Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 485 ASP 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 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 chunk 197 optimal weight: 0.4980 chunk 128 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.041823 restraints weight = 48358.719| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.54 r_work: 0.2538 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 17041 Z= 0.109 Angle : 0.619 15.952 23149 Z= 0.295 Chirality : 0.049 0.559 2616 Planarity : 0.003 0.044 2949 Dihedral : 8.170 82.581 2479 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.49 % Allowed : 22.17 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 2104 helix: 3.02 (0.27), residues: 370 sheet: 1.25 (0.19), residues: 738 loop : -1.48 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 274 HIS 0.001 0.000 HIS B 194 PHE 0.034 0.001 PHE D 403 TYR 0.010 0.001 TYR B 571 ARG 0.004 0.000 ARG B 451 Details of bonding type rmsd link_NAG-ASN : bond 0.01246 ( 4) link_NAG-ASN : angle 8.07571 ( 12) link_BETA1-4 : bond 0.02678 ( 4) link_BETA1-4 : angle 6.06430 ( 12) hydrogen bonds : bond 0.04010 ( 610) hydrogen bonds : angle 4.23923 ( 1710) SS BOND : bond 0.00398 ( 19) SS BOND : angle 1.39337 ( 38) covalent geometry : bond 0.00226 (17014) covalent geometry : angle 0.57233 (23087) ********************** 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 103 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8161 (ptm) REVERT: B 372 ARG cc_start: 0.9413 (mtt180) cc_final: 0.9050 (mmm160) REVERT: B 401 MET cc_start: 0.8479 (tpp) cc_final: 0.8052 (mmm) REVERT: B 603 MET cc_start: 0.8637 (mtt) cc_final: 0.8423 (mtt) REVERT: D 313 MET cc_start: 0.8731 (mmm) cc_final: 0.8436 (mmm) REVERT: D 372 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7854 (mmt90) REVERT: D 476 ARG cc_start: 0.9133 (mmm-85) cc_final: 0.8892 (mpp80) REVERT: D 572 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8855 (mptm) REVERT: F 142 THR cc_start: 0.4544 (OUTLIER) cc_final: 0.4272 (p) REVERT: F 313 MET cc_start: 0.8634 (mmp) cc_final: 0.8407 (mmp) REVERT: F 501 MET cc_start: 0.7773 (mtt) cc_final: 0.7547 (mmm) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 1.2040 time to fit residues: 137.8780 Evaluate side-chains 95 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 538 SER 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 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 485 ASP 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 88 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 548 HIS D 64 ASN ** 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 = 0.3130 r_free = 0.3130 target = 0.058920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.039489 restraints weight = 48629.412| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 3.52 r_work: 0.2469 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 17041 Z= 0.238 Angle : 0.683 15.905 23149 Z= 0.336 Chirality : 0.050 0.545 2616 Planarity : 0.004 0.046 2949 Dihedral : 8.210 83.034 2478 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.55 % Allowed : 22.33 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2104 helix: 2.83 (0.27), residues: 368 sheet: 1.11 (0.19), residues: 749 loop : -1.51 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 576 HIS 0.003 0.001 HIS B 194 PHE 0.026 0.002 PHE B 126 TYR 0.016 0.001 TYR B 446 ARG 0.005 0.000 ARG B 451 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 4) link_NAG-ASN : angle 8.08635 ( 12) link_BETA1-4 : bond 0.02643 ( 4) link_BETA1-4 : angle 5.96641 ( 12) hydrogen bonds : bond 0.04981 ( 610) hydrogen bonds : angle 4.52373 ( 1710) SS BOND : bond 0.00452 ( 19) SS BOND : angle 1.63994 ( 38) covalent geometry : bond 0.00569 (17014) covalent geometry : angle 0.64089 (23087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9967.88 seconds wall clock time: 173 minutes 6.22 seconds (10386.22 seconds total)