Starting phenix.real_space_refine on Fri Jul 3 22:36:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzb_36741/07_2026/8jzb_36741.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 Na 6 4.78 5 C 10548 2.51 5 N 2713 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "D" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "F" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "H" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4132 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 27, 'TRANS': 502} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 0 Ad-hoc single atom residues: {' NA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.20 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: 0.91 Conformation dependent library (CDL) restraints added in 710.9 milliseconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 25 sheets defined 19.4% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 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: 2.24 Time building geometry restraints manager: 1.23 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.840 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17041 Z= 0.453 Angle : 1.051 20.410 23149 Z= 0.671 Chirality : 0.065 0.895 2616 Planarity : 0.008 0.293 2949 Dihedral : 19.237 119.119 6405 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.14 % Favored : 97.72 % Rotamer: Outliers : 6.93 % Allowed : 19.40 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 364 sheet: 1.34 (0.19), residues: 754 loop : -1.47 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 398 TYR 0.034 0.002 TYR B 446 PHE 0.017 0.002 PHE H 126 TRP 0.016 0.002 TRP D 461 HIS 0.006 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.45 (17014) covalent geometry : angle 1.01638 / 0.67 (23087) SS BOND : bond 0.00606 / 0.38 ( 19) SS BOND : angle 1.58329 / 1.01 ( 38) hydrogen bonds : bond 0.15080 / 9.76 ( 610) hydrogen bonds : angle 6.13917 / 4.44 ( 1710) link_BETA1-4 : bond 0.02548 / 1.26 ( 4) link_BETA1-4 : angle 7.98295 / 5.20 ( 12) link_NAG-ASN : bond 0.01224 / 0.61 ( 4) link_NAG-ASN : angle 8.37538 / 5.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 98 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8869 (m) REVERT: B 359 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 603 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7826 (mtt) REVERT: D 83 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7044 (p0) REVERT: D 501 MET cc_start: 0.9042 (mmt) cc_final: 0.8327 (mmm) REVERT: F 460 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8775 (p) REVERT: H 78 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7936 (mp) outliers start: 130 outliers final: 40 residues processed: 210 average time/residue: 0.4737 time to fit residues: 112.3668 Evaluate side-chains 123 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 505 ILE Chi-restraints excluded: chain D residue 506 CYS Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 460 SER Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 429 SER Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 208 ASN B 359 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 263 GLN D 430 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN F 430 GLN H 64 ASN H 70 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 591 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.040306 restraints weight = 48569.734| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.54 r_work: 0.2483 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17041 Z= 0.243 Angle : 0.719 16.778 23149 Z= 0.356 Chirality : 0.055 0.794 2616 Planarity : 0.004 0.052 2949 Dihedral : 12.266 86.325 2548 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.05 % Allowed : 20.79 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2104 helix: 2.82 (0.27), residues: 367 sheet: 1.30 (0.19), residues: 751 loop : -1.55 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 476 TYR 0.015 0.001 TYR H 446 PHE 0.040 0.002 PHE D 403 TRP 0.011 0.002 TRP D 274 HIS 0.002 0.001 HIS H 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (17014) covalent geometry : angle 0.67076 / 0.34 (23087) SS BOND : bond 0.00473 / 0.26 ( 19) SS BOND : angle 1.61546 / 0.93 ( 38) hydrogen bonds : bond 0.05705 / 3.88 ( 610) hydrogen bonds : angle 4.94687 / 3.59 ( 1710) link_BETA1-4 : bond 0.02843 / 1.41 ( 4) link_BETA1-4 : angle 6.65811 / 4.70 ( 12) link_NAG-ASN : bond 0.01140 / 0.58 ( 4) link_NAG-ASN : angle 8.94035 / 5.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 79 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8252 (ptm160) REVERT: D 313 MET cc_start: 0.8661 (mmm) cc_final: 0.8270 (mpp) REVERT: H 135 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.9037 (tm-30) outliers start: 76 outliers final: 34 residues processed: 146 average time/residue: 0.4760 time to fit residues: 79.1324 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 : 0.615 ------------------------------------------------------------------------------- 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 565 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 584 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 502 CYS Chi-restraints excluded: chain F residue 514 ILE Chi-restraints excluded: chain H residue 72 GLN Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 71 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3154 r_free = 0.3154 target = 0.060162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.040668 restraints weight = 48821.101| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.55 r_work: 0.2500 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17041 Z= 0.151 Angle : 0.651 16.495 23149 Z= 0.314 Chirality : 0.052 0.731 2616 Planarity : 0.004 0.045 2949 Dihedral : 10.758 87.447 2497 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.93 % Allowed : 21.06 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2104 helix: 2.91 (0.27), residues: 368 sheet: 1.23 (0.19), residues: 753 loop : -1.52 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 476 TYR 0.013 0.001 TYR D 452 PHE 0.024 0.001 PHE H 126 TRP 0.010 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (17014) covalent geometry : angle 0.60169 / 0.30 (23087) SS BOND : bond 0.00430 / 0.26 ( 19) SS BOND : angle 1.44013 / 0.83 ( 38) hydrogen bonds : bond 0.05022 / 3.38 ( 610) hydrogen bonds : angle 4.64923 / 3.38 ( 1710) link_BETA1-4 : bond 0.02870 / 1.43 ( 4) link_BETA1-4 : angle 6.40435 / 4.59 ( 12) link_NAG-ASN : bond 0.01246 / 0.64 ( 4) link_NAG-ASN : angle 8.59143 / 5.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 81 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 451 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8204 (ptm160) REVERT: D 134 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: D 313 MET cc_start: 0.8671 (mmm) cc_final: 0.8201 (mpp) REVERT: H 250 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8918 (p) outliers start: 55 outliers final: 22 residues processed: 130 average time/residue: 0.4598 time to fit residues: 67.9353 Evaluate side-chains 98 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 71 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 485 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 89 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 18 optimal weight: 0.0060 chunk 12 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN D 71 GLN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.041849 restraints weight = 48416.287| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.47 r_work: 0.2530 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 17041 Z= 0.113 Angle : 0.617 16.212 23149 Z= 0.296 Chirality : 0.051 0.687 2616 Planarity : 0.004 0.038 2949 Dihedral : 9.545 86.282 2487 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.83 % Allowed : 20.68 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2104 helix: 2.87 (0.27), residues: 368 sheet: 1.27 (0.19), residues: 750 loop : -1.51 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 476 TYR 0.011 0.001 TYR D 452 PHE 0.038 0.001 PHE D 403 TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17014) covalent geometry : angle 0.56674 / 0.28 (23087) SS BOND : bond 0.00348 / 0.18 ( 19) SS BOND : angle 1.36843 / 0.74 ( 38) hydrogen bonds : bond 0.04477 / 3.01 ( 610) hydrogen bonds : angle 4.44565 / 3.23 ( 1710) link_BETA1-4 : bond 0.02788 / 1.39 ( 4) link_BETA1-4 : angle 6.28361 / 4.55 ( 12) link_NAG-ASN : bond 0.01264 / 0.65 ( 4) link_NAG-ASN : angle 8.49013 / 5.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 77 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8382 (ptp) cc_final: 0.7997 (ppp) REVERT: B 451 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8254 (ptm160) REVERT: D 313 MET cc_start: 0.8684 (mmm) cc_final: 0.8184 (mpp) REVERT: D 372 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8054 (mmt90) REVERT: D 437 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8889 (p) REVERT: D 476 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8720 (mpp80) REVERT: F 142 THR cc_start: 0.4845 (OUTLIER) cc_final: 0.4627 (p) REVERT: F 313 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (mmp) REVERT: H 250 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8941 (p) outliers start: 53 outliers final: 23 residues processed: 121 average time/residue: 0.4384 time to fit residues: 60.5919 Evaluate side-chains 102 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 75 LEU 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 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 61 optimal weight: 0.0870 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 GLN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.041440 restraints weight = 48242.666| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.49 r_work: 0.2502 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17041 Z= 0.116 Angle : 0.601 16.172 23149 Z= 0.287 Chirality : 0.050 0.647 2616 Planarity : 0.003 0.042 2949 Dihedral : 9.129 85.100 2483 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.77 % Allowed : 20.90 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2104 helix: 2.87 (0.27), residues: 371 sheet: 1.26 (0.19), residues: 749 loop : -1.48 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 476 TYR 0.011 0.001 TYR H 446 PHE 0.028 0.001 PHE D 403 TRP 0.007 0.001 TRP D 274 HIS 0.002 0.000 HIS H 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17014) covalent geometry : angle 0.55056 / 0.27 (23087) SS BOND : bond 0.00327 / 0.18 ( 19) SS BOND : angle 1.44372 / 0.83 ( 38) hydrogen bonds : bond 0.04337 / 2.90 ( 610) hydrogen bonds : angle 4.34361 / 3.17 ( 1710) link_BETA1-4 : bond 0.02802 / 1.40 ( 4) link_BETA1-4 : angle 6.22805 / 4.52 ( 12) link_NAG-ASN : bond 0.01268 / 0.65 ( 4) link_NAG-ASN : angle 8.32855 / 4.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 74 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8513 (ptp) cc_final: 0.8125 (ppp) REVERT: B 401 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: B 451 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8238 (ptm160) REVERT: B 603 MET cc_start: 0.8544 (mtt) cc_final: 0.8227 (mtt) REVERT: D 85 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8067 (pmtt) REVERT: D 134 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8697 (tp30) REVERT: D 313 MET cc_start: 0.8815 (mmm) cc_final: 0.8486 (mmm) REVERT: D 372 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8070 (mmt90) REVERT: F 142 THR cc_start: 0.4708 (OUTLIER) cc_final: 0.4459 (p) REVERT: F 313 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8486 (mmp) REVERT: H 250 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9149 (p) outliers start: 52 outliers final: 19 residues processed: 121 average time/residue: 0.4884 time to fit residues: 66.3585 Evaluate side-chains 99 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR 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 134 GLU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 137 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 28 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN ** D 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 = 0.3144 r_free = 0.3144 target = 0.059523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.040082 restraints weight = 48540.670| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.54 r_work: 0.2486 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17041 Z= 0.199 Angle : 0.644 16.074 23149 Z= 0.313 Chirality : 0.050 0.627 2616 Planarity : 0.004 0.038 2949 Dihedral : 8.950 84.498 2482 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 21.00 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2104 helix: 2.86 (0.27), residues: 370 sheet: 1.22 (0.19), residues: 741 loop : -1.52 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 509 TYR 0.014 0.001 TYR B 446 PHE 0.025 0.002 PHE D 403 TRP 0.008 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (17014) covalent geometry : angle 0.59782 / 0.30 (23087) SS BOND : bond 0.00209 / 0.13 ( 19) SS BOND : angle 1.40567 / 0.82 ( 38) hydrogen bonds : bond 0.04819 / 3.27 ( 610) hydrogen bonds : angle 4.47414 / 3.27 ( 1710) link_BETA1-4 : bond 0.02696 / 1.34 ( 4) link_BETA1-4 : angle 6.13483 / 4.43 ( 12) link_NAG-ASN : bond 0.01219 / 0.63 ( 4) link_NAG-ASN : angle 8.28487 / 4.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 74 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8488 (ptp) cc_final: 0.8081 (ppp) REVERT: B 401 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: B 451 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8278 (ptm160) REVERT: B 603 MET cc_start: 0.8417 (mtt) cc_final: 0.8004 (mtt) REVERT: D 313 MET cc_start: 0.8774 (mmm) cc_final: 0.8383 (mmm) REVERT: D 372 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8022 (mmt90) REVERT: F 142 THR cc_start: 0.4552 (OUTLIER) cc_final: 0.4309 (p) REVERT: F 313 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8380 (mmp) REVERT: H 250 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.9067 (p) outliers start: 50 outliers final: 28 residues processed: 117 average time/residue: 0.4981 time to fit residues: 65.9882 Evaluate side-chains 108 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 451 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 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 441 SER Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 137 ILE 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 Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.040367 restraints weight = 48225.674| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.53 r_work: 0.2498 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17041 Z= 0.154 Angle : 0.625 16.062 23149 Z= 0.301 Chirality : 0.050 0.602 2616 Planarity : 0.004 0.041 2949 Dihedral : 8.722 83.949 2482 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2104 helix: 2.94 (0.27), residues: 370 sheet: 1.18 (0.19), residues: 740 loop : -1.53 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 451 TYR 0.011 0.001 TYR H 446 PHE 0.023 0.001 PHE D 403 TRP 0.009 0.001 TRP D 274 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (17014) covalent geometry : angle 0.57809 / 0.29 (23087) SS BOND : bond 0.00453 / 0.23 ( 19) SS BOND : angle 1.39021 / 0.77 ( 38) hydrogen bonds : bond 0.04590 / 3.09 ( 610) hydrogen bonds : angle 4.39662 / 3.21 ( 1710) link_BETA1-4 : bond 0.02710 / 1.35 ( 4) link_BETA1-4 : angle 6.11617 / 4.41 ( 12) link_NAG-ASN : bond 0.01226 / 0.63 ( 4) link_NAG-ASN : angle 8.22467 / 4.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8437 (ptp) cc_final: 0.8063 (ppp) REVERT: B 401 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7959 (mmm) REVERT: B 603 MET cc_start: 0.8451 (mtt) cc_final: 0.8022 (mtt) REVERT: D 313 MET cc_start: 0.8778 (mmm) cc_final: 0.8379 (mmm) REVERT: D 372 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7996 (mmt90) REVERT: D 572 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8910 (mptm) REVERT: F 142 THR cc_start: 0.4515 (OUTLIER) cc_final: 0.4270 (p) REVERT: F 313 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8472 (mmp) REVERT: H 99 GLU cc_start: 0.8673 (tt0) cc_final: 0.8178 (tm-30) REVERT: H 250 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.9081 (p) REVERT: H 401 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8073 (mpp) outliers start: 42 outliers final: 24 residues processed: 115 average time/residue: 0.5696 time to fit residues: 73.8308 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 : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain D residue 75 LEU 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 401 MET 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 D residue 572 LYS Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 401 MET Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Chi-restraints excluded: chain H residue 497 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 6 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 173 optimal weight: 0.0020 chunk 100 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN D 64 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.040482 restraints weight = 48659.662| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.55 r_work: 0.2499 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2107 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= 0.147 Angle : 0.632 16.043 23149 Z= 0.305 Chirality : 0.049 0.584 2616 Planarity : 0.004 0.043 2949 Dihedral : 8.529 83.741 2480 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.29 % Allowed : 21.11 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2104 helix: 2.92 (0.27), residues: 368 sheet: 1.19 (0.19), residues: 741 loop : -1.53 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 451 TYR 0.011 0.001 TYR H 446 PHE 0.025 0.001 PHE F 89 TRP 0.009 0.001 TRP D 461 HIS 0.002 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (17014) covalent geometry : angle 0.58610 / 0.29 (23087) SS BOND : bond 0.00407 / 0.21 ( 19) SS BOND : angle 1.33802 / 0.74 ( 38) hydrogen bonds : bond 0.04512 / 3.04 ( 610) hydrogen bonds : angle 4.42238 / 3.24 ( 1710) link_BETA1-4 : bond 0.02746 / 1.37 ( 4) link_BETA1-4 : angle 6.09077 / 4.37 ( 12) link_NAG-ASN : bond 0.01218 / 0.63 ( 4) link_NAG-ASN : angle 8.17754 / 4.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 75 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8435 (ptp) cc_final: 0.8051 (ppp) REVERT: B 313 MET cc_start: 0.8151 (mmm) cc_final: 0.7527 (mpp) REVERT: B 371 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8253 (p0) REVERT: B 372 ARG cc_start: 0.9415 (mtt180) cc_final: 0.9154 (mmm160) REVERT: B 401 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7793 (mmm) REVERT: B 603 MET cc_start: 0.8483 (mtt) cc_final: 0.8031 (mtt) REVERT: D 313 MET cc_start: 0.8791 (mmm) cc_final: 0.8474 (mmm) REVERT: D 372 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7992 (mmt90) REVERT: D 572 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8910 (mptm) REVERT: F 88 MET cc_start: 0.8567 (ptm) cc_final: 0.8273 (ttp) REVERT: F 142 THR cc_start: 0.4487 (OUTLIER) cc_final: 0.4243 (p) REVERT: F 313 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8454 (mmp) REVERT: H 74 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8629 (tpp) REVERT: H 99 GLU cc_start: 0.8669 (tt0) cc_final: 0.8187 (tm-30) REVERT: H 250 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9068 (p) REVERT: H 401 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7993 (mpp) outliers start: 43 outliers final: 27 residues processed: 110 average time/residue: 0.5036 time to fit residues: 62.8383 Evaluate side-chains 108 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 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 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 572 LYS Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 188 CYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 137 ILE 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 401 MET Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 8.9990 chunk 144 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 146 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.040866 restraints weight = 48619.794| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.54 r_work: 0.2511 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 0.066 17041 Z= 0.123 Angle : 0.630 16.005 23149 Z= 0.302 Chirality : 0.049 0.570 2616 Planarity : 0.003 0.041 2949 Dihedral : 8.383 83.313 2480 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.13 % Allowed : 21.11 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2104 helix: 2.92 (0.27), residues: 370 sheet: 1.19 (0.19), residues: 739 loop : -1.47 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 372 TYR 0.010 0.001 TYR H 446 PHE 0.026 0.001 PHE F 89 TRP 0.010 0.001 TRP D 461 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (17014) covalent geometry : angle 0.58362 / 0.29 (23087) SS BOND : bond 0.00399 / 0.21 ( 19) SS BOND : angle 1.63008 / 1.19 ( 38) hydrogen bonds : bond 0.04350 / 2.93 ( 610) hydrogen bonds : angle 4.36539 / 3.19 ( 1710) link_BETA1-4 : bond 0.02713 / 1.35 ( 4) link_BETA1-4 : angle 6.07272 / 4.35 ( 12) link_NAG-ASN : bond 0.01224 / 0.63 ( 4) link_NAG-ASN : angle 8.11462 / 4.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8442 (ptp) cc_final: 0.8058 (ppp) REVERT: B 313 MET cc_start: 0.8127 (mmm) cc_final: 0.7514 (mpp) REVERT: B 371 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8211 (p0) REVERT: B 372 ARG cc_start: 0.9409 (mtt180) cc_final: 0.9175 (mmm160) REVERT: B 401 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: B 603 MET cc_start: 0.8508 (mtt) cc_final: 0.8049 (mtt) REVERT: D 313 MET cc_start: 0.8766 (mmm) cc_final: 0.8469 (mmm) REVERT: D 372 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8009 (mmt90) REVERT: D 572 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8855 (mptm) REVERT: F 88 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8375 (ttp) REVERT: F 142 THR cc_start: 0.4489 (OUTLIER) cc_final: 0.4243 (p) REVERT: F 313 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8452 (mmp) REVERT: H 74 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8524 (tpp) REVERT: H 99 GLU cc_start: 0.8561 (tt0) cc_final: 0.8060 (tm-30) REVERT: H 250 SER cc_start: 0.9331 (OUTLIER) cc_final: 0.9084 (p) REVERT: H 401 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7962 (mpp) outliers start: 40 outliers final: 21 residues processed: 103 average time/residue: 0.5163 time to fit residues: 60.3365 Evaluate side-chains 102 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 572 LYS Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 401 MET Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 153 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.041227 restraints weight = 48540.191| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.54 r_work: 0.2523 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17041 Z= 0.119 Angle : 0.625 15.989 23149 Z= 0.299 Chirality : 0.049 0.556 2616 Planarity : 0.003 0.045 2949 Dihedral : 8.189 82.833 2479 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.76 % Allowed : 21.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2104 helix: 2.94 (0.27), residues: 370 sheet: 1.25 (0.19), residues: 727 loop : -1.45 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.010 0.001 TYR H 446 PHE 0.027 0.001 PHE B 126 TRP 0.008 0.001 TRP D 461 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17014) covalent geometry : angle 0.57883 / 0.29 (23087) SS BOND : bond 0.00400 / 0.21 ( 19) SS BOND : angle 1.54405 / 1.09 ( 38) hydrogen bonds : bond 0.04185 / 2.82 ( 610) hydrogen bonds : angle 4.30856 / 3.15 ( 1710) link_BETA1-4 : bond 0.02679 / 1.34 ( 4) link_BETA1-4 : angle 6.04793 / 4.32 ( 12) link_NAG-ASN : bond 0.01204 / 0.62 ( 4) link_NAG-ASN : angle 8.03441 / 4.79 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8420 (ptp) cc_final: 0.8042 (ppp) REVERT: B 313 MET cc_start: 0.8110 (mmm) cc_final: 0.7499 (mpp) REVERT: B 372 ARG cc_start: 0.9377 (mtt180) cc_final: 0.9101 (mmm160) REVERT: B 401 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7899 (mmm) REVERT: B 603 MET cc_start: 0.8534 (mtt) cc_final: 0.8067 (mtt) REVERT: D 313 MET cc_start: 0.8762 (mmm) cc_final: 0.8444 (mmm) REVERT: D 372 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8000 (mmt90) REVERT: F 88 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: F 142 THR cc_start: 0.4455 (OUTLIER) cc_final: 0.4207 (p) REVERT: F 313 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8436 (mmp) REVERT: H 74 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (tpp) REVERT: H 99 GLU cc_start: 0.8549 (tt0) cc_final: 0.8056 (tm-30) REVERT: H 250 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.9118 (p) REVERT: H 401 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7931 (mpp) outliers start: 33 outliers final: 21 residues processed: 98 average time/residue: 0.4982 time to fit residues: 55.2050 Evaluate side-chains 100 residues out of total 1876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 484 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain H residue 401 MET Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain H residue 470 THR Chi-restraints excluded: chain H residue 492 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 371 ASN ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041108 restraints weight = 48279.591| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.51 r_work: 0.2510 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17041 Z= 0.132 Angle : 0.618 15.910 23149 Z= 0.297 Chirality : 0.049 0.543 2616 Planarity : 0.003 0.044 2949 Dihedral : 8.012 82.343 2479 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 21.70 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2104 helix: 2.90 (0.27), residues: 369 sheet: 1.20 (0.19), residues: 741 loop : -1.43 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.011 0.001 TYR H 446 PHE 0.028 0.001 PHE B 126 TRP 0.009 0.001 TRP H 461 HIS 0.001 0.000 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17014) covalent geometry : angle 0.57139 / 0.29 (23087) SS BOND : bond 0.00397 / 0.20 ( 19) SS BOND : angle 1.52887 / 1.06 ( 38) hydrogen bonds : bond 0.04253 / 2.88 ( 610) hydrogen bonds : angle 4.31072 / 3.16 ( 1710) link_BETA1-4 : bond 0.02661 / 1.33 ( 4) link_BETA1-4 : angle 6.01678 / 4.29 ( 12) link_NAG-ASN : bond 0.01221 / 0.63 ( 4) link_NAG-ASN : angle 8.01753 / 4.77 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.18 seconds wall clock time: 75 minutes 37.16 seconds (4537.16 seconds total)