Starting phenix.real_space_refine on Sun Sep 13 13:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uz8_20953/09_2026/6uz8_20953.cif" } resolution = 2.84 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 140 5.16 5 Cl 4 4.86 5 C 15280 2.51 5 N 3828 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "D" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "B" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "C" Number of atoms: 5693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 734, 5686 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 21, 'GLN:plan1': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 5801 Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'R0D': 1, 'SBM': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.70, per 1000 atoms: 0.42 Number of scatterers: 23320 At special positions: 0 Unit cell: (128.544, 128.544, 173.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 140 16.00 P 4 15.00 O 4064 8.00 N 3828 7.00 C 15280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 258 " distance=2.04 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 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 71.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 4.085A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 438 through 460 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 465 " --> pdb=" O ALA A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.090A pdb=" N LYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP A 514 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 3.506A pdb=" N TYR A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER A 595 " --> pdb=" O PRO A 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.675A pdb=" N ILE A 610 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL A 691 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 692 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 732 " --> pdb=" O ASN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 752 removed outlier: 3.510A pdb=" N GLU A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.971A pdb=" N PHE D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 135 through 143 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.638A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 removed outlier: 4.084A pdb=" N TYR D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 329 " --> pdb=" O CYS D 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU D 368 " --> pdb=" O SER D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.875A pdb=" N LEU D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 Processing helix chain 'D' and resid 438 through 460 Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.767A pdb=" N ARG D 464 " --> pdb=" O ALA D 461 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 465 " --> pdb=" O ALA D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 461 through 465' Processing helix chain 'D' and resid 483 through 488 removed outlier: 4.090A pdb=" N LYS D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 488 " --> pdb=" O PHE D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 483 through 488' Processing helix chain 'D' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP D 514 " --> pdb=" O CYS D 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Proline residue: D 518 - end of helix removed outlier: 3.506A pdb=" N TYR D 521 " --> pdb=" O GLY D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER D 595 " --> pdb=" O PRO D 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 617 removed outlier: 3.675A pdb=" N ILE D 610 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 611 " --> pdb=" O SER D 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL D 691 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 692 " --> pdb=" O LYS D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU D 701 " --> pdb=" O HIS D 697 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 732 " --> pdb=" O ASN D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 752 removed outlier: 3.509A pdb=" N GLU D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 912 " --> pdb=" O ASP D 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 257 through 265 removed outlier: 3.667A pdb=" N LYS B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 removed outlier: 4.084A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 329 " --> pdb=" O CYS B 325 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 3.507A pdb=" N LEU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.603A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 438 through 460 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 465 " --> pdb=" O ALA B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 465' Processing helix chain 'B' and resid 483 through 488 removed outlier: 4.089A pdb=" N LYS B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 488 " --> pdb=" O PHE B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 488' Processing helix chain 'B' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP B 514 " --> pdb=" O CYS B 510 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 3.505A pdb=" N TYR B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 558 removed outlier: 3.842A pdb=" N LEU B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER B 595 " --> pdb=" O PRO B 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.674A pdb=" N ILE B 610 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 611 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 636 through 657 removed outlier: 3.980A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.924A pdb=" N TRP B 680 " --> pdb=" O LYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.735A pdb=" N VAL B 691 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 692 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 752 removed outlier: 3.509A pdb=" N GLU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 918 removed outlier: 3.905A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 912 " --> pdb=" O ASP B 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.970A pdb=" N PHE C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 160 through 172 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.668A pdb=" N LYS C 261 " --> pdb=" O ASP C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.776A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.639A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 removed outlier: 4.085A pdb=" N TYR C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 329 " --> pdb=" O CYS C 325 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.649A pdb=" N VAL C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 removed outlier: 3.508A pdb=" N LEU C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.604A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 393 removed outlier: 4.004A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.876A pdb=" N LEU C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 438 through 460 Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.768A pdb=" N ARG C 464 " --> pdb=" O ALA C 461 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 461 through 465' Processing helix chain 'C' and resid 483 through 488 removed outlier: 4.089A pdb=" N LYS C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 488 " --> pdb=" O PHE C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 483 through 488' Processing helix chain 'C' and resid 492 through 521 removed outlier: 3.767A pdb=" N GLU C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TRP C 514 " --> pdb=" O CYS C 510 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Proline residue: C 518 - end of helix removed outlier: 3.506A pdb=" N TYR C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 558 removed outlier: 3.843A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 606 removed outlier: 3.750A pdb=" N SER C 595 " --> pdb=" O PRO C 591 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.676A pdb=" N ILE C 610 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 611 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.652A pdb=" N GLN C 624 " --> pdb=" O PHE C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 636 through 657 removed outlier: 3.981A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.923A pdb=" N TRP C 680 " --> pdb=" O LYS C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 removed outlier: 3.736A pdb=" N VAL C 691 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 692 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 732 removed outlier: 3.580A pdb=" N GLU C 701 " --> pdb=" O HIS C 697 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 752 removed outlier: 3.510A pdb=" N GLU C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 918 removed outlier: 3.906A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU C 912 " --> pdb=" O ASP C 908 " (cutoff:3.500A) 1340 hydrogen bonds defined for protein. 3980 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: 4.27 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3652 1.31 - 1.44: 6468 1.44 - 1.56: 13384 1.56 - 1.69: 108 1.69 - 1.82: 248 Bond restraints: 23860 Sorted by residual: bond pdb=" C07 R0D D1003 " pdb=" N06 R0D D1003 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D B1001 " pdb=" N06 R0D B1001 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D C1001 " pdb=" N06 R0D C1001 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C07 R0D A1003 " pdb=" N06 R0D A1003 " ideal model delta sigma weight residual 1.278 1.468 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" O5 SBM C1003 " pdb=" P SBM C1003 " ideal model delta sigma weight residual 1.648 1.777 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 23855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 31672 3.09 - 6.17: 584 6.17 - 9.26: 80 9.26 - 12.35: 32 12.35 - 15.44: 12 Bond angle restraints: 32380 Sorted by residual: angle pdb=" C ASN D 110 " pdb=" N ILE D 111 " pdb=" CA ILE D 111 " ideal model delta sigma weight residual 120.24 124.25 -4.01 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN A 110 " pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta sigma weight residual 120.24 124.25 -4.01 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN C 110 " pdb=" N ILE C 111 " pdb=" CA ILE C 111 " ideal model delta sigma weight residual 120.24 124.24 -4.00 6.30e-01 2.52e+00 4.04e+01 angle pdb=" C ASN B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.24 124.24 -4.00 6.30e-01 2.52e+00 4.04e+01 angle pdb=" N ASN C 125 " pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " ideal model delta sigma weight residual 110.37 101.13 9.24 1.65e+00 3.67e-01 3.13e+01 ... (remaining 32375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 13816 35.90 - 71.80: 228 71.80 - 107.71: 8 107.71 - 143.61: 0 143.61 - 179.51: 4 Dihedral angle restraints: 14056 sinusoidal: 5396 harmonic: 8660 Sorted by residual: dihedral pdb=" N ASN C 125 " pdb=" C ASN C 125 " pdb=" CA ASN C 125 " pdb=" CB ASN C 125 " ideal model delta harmonic sigma weight residual 122.80 107.99 14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" N ASN A 125 " pdb=" C ASN A 125 " pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " ideal model delta harmonic sigma weight residual 122.80 108.00 14.80 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" N ASN B 125 " pdb=" C ASN B 125 " pdb=" CA ASN B 125 " pdb=" CB ASN B 125 " ideal model delta harmonic sigma weight residual 122.80 108.00 14.80 0 2.50e+00 1.60e-01 3.50e+01 ... (remaining 14053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3377 0.090 - 0.180: 235 0.180 - 0.270: 36 0.270 - 0.360: 24 0.360 - 0.450: 4 Chirality restraints: 3676 Sorted by residual: chirality pdb=" C2 SBM D1001 " pdb=" C1 SBM D1001 " pdb=" C3 SBM D1001 " pdb=" O2 SBM D1001 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C2 SBM B1003 " pdb=" C1 SBM B1003 " pdb=" C3 SBM B1003 " pdb=" O2 SBM B1003 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C2 SBM A1001 " pdb=" C1 SBM A1001 " pdb=" C3 SBM A1001 " pdb=" O2 SBM A1001 " both_signs ideal model delta sigma weight residual False 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.03e+00 ... (remaining 3673 not shown) Planarity restraints: 3992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 R0D B1001 " 0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D B1001 " -0.002 2.00e-02 2.50e+03 pdb=" C04 R0D B1001 " -0.007 2.00e-02 2.50e+03 pdb=" C05 R0D B1001 " -0.007 2.00e-02 2.50e+03 pdb=" C07 R0D B1001 " 0.169 2.00e-02 2.50e+03 pdb=" C08 R0D B1001 " -0.006 2.00e-02 2.50e+03 pdb=" C09 R0D B1001 " 1.156 2.00e-02 2.50e+03 pdb=" C25 R0D B1001 " -1.318 2.00e-02 2.50e+03 pdb=" C26 R0D B1001 " 0.002 2.00e-02 2.50e+03 pdb=" C27 R0D B1001 " 0.005 2.00e-02 2.50e+03 pdb=" N06 R0D B1001 " -0.011 2.00e-02 2.50e+03 pdb="CL01 R0D B1001 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D C1001 " -0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D C1001 " 0.002 2.00e-02 2.50e+03 pdb=" C04 R0D C1001 " 0.007 2.00e-02 2.50e+03 pdb=" C05 R0D C1001 " 0.007 2.00e-02 2.50e+03 pdb=" C07 R0D C1001 " -0.169 2.00e-02 2.50e+03 pdb=" C08 R0D C1001 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R0D C1001 " -1.156 2.00e-02 2.50e+03 pdb=" C25 R0D C1001 " 1.318 2.00e-02 2.50e+03 pdb=" C26 R0D C1001 " -0.002 2.00e-02 2.50e+03 pdb=" C27 R0D C1001 " -0.005 2.00e-02 2.50e+03 pdb=" N06 R0D C1001 " 0.011 2.00e-02 2.50e+03 pdb="CL01 R0D C1001 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D D1003 " -0.005 2.00e-02 2.50e+03 5.08e-01 7.76e+03 pdb=" C03 R0D D1003 " 0.001 2.00e-02 2.50e+03 pdb=" C04 R0D D1003 " 0.007 2.00e-02 2.50e+03 pdb=" C05 R0D D1003 " 0.007 2.00e-02 2.50e+03 pdb=" C07 R0D D1003 " -0.169 2.00e-02 2.50e+03 pdb=" C08 R0D D1003 " 0.006 2.00e-02 2.50e+03 pdb=" C09 R0D D1003 " -1.156 2.00e-02 2.50e+03 pdb=" C25 R0D D1003 " 1.318 2.00e-02 2.50e+03 pdb=" C26 R0D D1003 " -0.002 2.00e-02 2.50e+03 pdb=" C27 R0D D1003 " -0.005 2.00e-02 2.50e+03 pdb=" N06 R0D D1003 " 0.011 2.00e-02 2.50e+03 pdb="CL01 R0D D1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 3989 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6997 2.82 - 3.34: 20229 3.34 - 3.86: 37007 3.86 - 4.38: 44278 4.38 - 4.90: 75585 Nonbonded interactions: 184096 Sorted by model distance: nonbonded pdb=" OD1 ASP D 265 " pdb=" OG1 THR C 339 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" OD1 ASP B 265 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR B 339 " pdb=" OD1 ASP C 265 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP A 265 " pdb=" OG1 THR D 339 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR C 656 " pdb=" O VAL C 691 " model vdw 2.320 3.040 ... (remaining 184091 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'B' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'C' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) selection = (chain 'D' and (resid 85 through 445 or resid 447 through 920 or resid 1002 or r \ esid 1004)) } 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=0.50 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: 1.670 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.930 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.008 0.190 23864 Z= 0.403 Angle : 1.046 15.437 32388 Z= 0.524 Chirality : 0.059 0.450 3676 Planarity : 0.018 0.508 3992 Dihedral : 13.812 179.509 8428 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.21 % Cbeta Deviations : 0.14 % 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: -3.69 (0.12), residues: 2908 helix: -2.19 (0.09), residues: 2020 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 583 TYR 0.039 0.003 TYR D 209 PHE 0.022 0.002 PHE C 537 TRP 0.018 0.002 TRP D 391 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.40 (23860) covalent geometry : angle 1.04578 / 0.52 (32380) SS BOND : bond 0.00657 / 0.30 ( 4) SS BOND : angle 0.61085 / 0.35 ( 8) hydrogen bonds : bond 0.13729 / 9.37 ( 1340) hydrogen bonds : angle 5.50010 / 3.98 ( 3980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 393 time to evaluate : 0.870 Fit side-chains REVERT: A 131 TYR cc_start: 0.8502 (p90) cc_final: 0.8010 (p90) REVERT: A 393 GLU cc_start: 0.7029 (tt0) cc_final: 0.6724 (tt0) REVERT: A 407 PHE cc_start: 0.7113 (t80) cc_final: 0.6749 (m-80) REVERT: A 441 MET cc_start: 0.8128 (mmm) cc_final: 0.7899 (mmm) REVERT: A 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7895 (mmm) REVERT: A 494 MET cc_start: 0.7500 (mtt) cc_final: 0.7204 (mmm) REVERT: A 524 GLU cc_start: 0.7947 (tt0) cc_final: 0.7674 (tt0) REVERT: A 530 ASP cc_start: 0.7581 (m-30) cc_final: 0.7335 (m-30) REVERT: A 643 MET cc_start: 0.8358 (mtt) cc_final: 0.7904 (mtt) REVERT: A 666 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 878 GLU cc_start: 0.6566 (pt0) cc_final: 0.6263 (pt0) REVERT: D 131 TYR cc_start: 0.8508 (p90) cc_final: 0.8056 (p90) REVERT: D 393 GLU cc_start: 0.7038 (tt0) cc_final: 0.6731 (tt0) REVERT: D 407 PHE cc_start: 0.7124 (t80) cc_final: 0.6749 (m-80) REVERT: D 441 MET cc_start: 0.8128 (mmm) cc_final: 0.7903 (mmm) REVERT: D 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7903 (mmm) REVERT: D 494 MET cc_start: 0.7507 (mtt) cc_final: 0.7205 (mmm) REVERT: D 524 GLU cc_start: 0.7949 (tt0) cc_final: 0.7677 (tt0) REVERT: D 530 ASP cc_start: 0.7578 (m-30) cc_final: 0.7338 (m-30) REVERT: D 643 MET cc_start: 0.8391 (mtt) cc_final: 0.7935 (mtt) REVERT: D 666 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7538 (mm-30) REVERT: D 878 GLU cc_start: 0.6561 (pt0) cc_final: 0.6260 (pt0) REVERT: B 131 TYR cc_start: 0.8508 (p90) cc_final: 0.8004 (p90) REVERT: B 393 GLU cc_start: 0.7032 (tt0) cc_final: 0.6726 (tt0) REVERT: B 407 PHE cc_start: 0.7114 (t80) cc_final: 0.6750 (m-80) REVERT: B 441 MET cc_start: 0.8130 (mmm) cc_final: 0.7902 (mmm) REVERT: B 486 MET cc_start: 0.8126 (mmm) cc_final: 0.7902 (mmm) REVERT: B 494 MET cc_start: 0.7495 (mtt) cc_final: 0.7196 (mmm) REVERT: B 524 GLU cc_start: 0.7948 (tt0) cc_final: 0.7675 (tt0) REVERT: B 530 ASP cc_start: 0.7584 (m-30) cc_final: 0.7336 (m-30) REVERT: B 643 MET cc_start: 0.8358 (mtt) cc_final: 0.7905 (mtt) REVERT: B 666 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 878 GLU cc_start: 0.6570 (pt0) cc_final: 0.6266 (pt0) REVERT: C 131 TYR cc_start: 0.8522 (p90) cc_final: 0.8043 (p90) REVERT: C 393 GLU cc_start: 0.7029 (tt0) cc_final: 0.6719 (tt0) REVERT: C 407 PHE cc_start: 0.7215 (t80) cc_final: 0.6671 (m-80) REVERT: C 441 MET cc_start: 0.8131 (mmm) cc_final: 0.7901 (mmm) REVERT: C 486 MET cc_start: 0.8120 (mmm) cc_final: 0.7889 (mmm) REVERT: C 494 MET cc_start: 0.7501 (mtt) cc_final: 0.7193 (mmm) REVERT: C 524 GLU cc_start: 0.7950 (tt0) cc_final: 0.7676 (tt0) REVERT: C 530 ASP cc_start: 0.7585 (m-30) cc_final: 0.7340 (m-30) REVERT: C 643 MET cc_start: 0.8357 (mtt) cc_final: 0.7903 (mtt) REVERT: C 666 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 878 GLU cc_start: 0.6589 (pt0) cc_final: 0.6296 (pt0) outliers start: 4 outliers final: 8 residues processed: 397 average time/residue: 0.6501 time to fit residues: 293.3560 Evaluate side-chains 306 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 298 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 HIS A 732 GLN D 380 HIS D 732 GLN B 380 HIS B 732 GLN C 260 GLN C 380 HIS C 732 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106582 restraints weight = 57302.157| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.60 r_work: 0.2989 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23864 Z= 0.117 Angle : 1.046 60.247 32388 Z= 0.410 Chirality : 0.038 0.124 3676 Planarity : 0.005 0.055 3992 Dihedral : 10.370 122.393 3400 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 10.73 % Favored : 88.74 % 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: -1.12 (0.14), residues: 2908 helix: -0.06 (0.11), residues: 2036 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 865 TYR 0.021 0.001 TYR A 705 PHE 0.009 0.001 PHE A 675 TRP 0.017 0.001 TRP C 391 HIS 0.002 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (23860) covalent geometry : angle 1.04608 / 0.41 (32380) SS BOND : bond 0.00322 / 0.15 ( 4) SS BOND : angle 0.18380 / 0.11 ( 8) hydrogen bonds : bond 0.04458 / 3.05 ( 1340) hydrogen bonds : angle 3.50753 / 2.54 ( 3980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 286 time to evaluate : 0.840 Fit side-chains REVERT: A 130 ASP cc_start: 0.8280 (t0) cc_final: 0.7967 (t0) REVERT: A 407 PHE cc_start: 0.7299 (t80) cc_final: 0.6685 (m-80) REVERT: A 441 MET cc_start: 0.8757 (mmm) cc_final: 0.8425 (mmm) REVERT: A 494 MET cc_start: 0.7968 (mtt) cc_final: 0.7706 (mmm) REVERT: A 524 GLU cc_start: 0.7861 (tt0) cc_final: 0.7571 (tt0) REVERT: A 643 MET cc_start: 0.8957 (mtt) cc_final: 0.8714 (mtt) REVERT: A 666 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8267 (mm-30) REVERT: D 130 ASP cc_start: 0.8298 (t0) cc_final: 0.7946 (t0) REVERT: D 407 PHE cc_start: 0.7294 (t80) cc_final: 0.6670 (m-80) REVERT: D 441 MET cc_start: 0.8750 (mmm) cc_final: 0.8419 (mmm) REVERT: D 494 MET cc_start: 0.7968 (mtt) cc_final: 0.7703 (mmm) REVERT: D 524 GLU cc_start: 0.7847 (tt0) cc_final: 0.7554 (tt0) REVERT: D 643 MET cc_start: 0.8944 (mtt) cc_final: 0.8696 (mtt) REVERT: D 666 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 859 MET cc_start: 0.8877 (mmm) cc_final: 0.8652 (mmm) REVERT: B 130 ASP cc_start: 0.8268 (t0) cc_final: 0.7946 (t0) REVERT: B 407 PHE cc_start: 0.7307 (t80) cc_final: 0.6686 (m-80) REVERT: B 441 MET cc_start: 0.8746 (mmm) cc_final: 0.8416 (mmm) REVERT: B 494 MET cc_start: 0.7983 (mtt) cc_final: 0.7726 (mmm) REVERT: B 524 GLU cc_start: 0.7860 (tt0) cc_final: 0.7573 (tt0) REVERT: B 643 MET cc_start: 0.8942 (mtt) cc_final: 0.8696 (mtt) REVERT: B 666 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8254 (mm-30) REVERT: C 130 ASP cc_start: 0.8238 (t0) cc_final: 0.7900 (t0) REVERT: C 407 PHE cc_start: 0.7276 (t80) cc_final: 0.6676 (m-80) REVERT: C 441 MET cc_start: 0.8749 (mmm) cc_final: 0.8417 (mmm) REVERT: C 494 MET cc_start: 0.7950 (mtt) cc_final: 0.7697 (mmm) REVERT: C 524 GLU cc_start: 0.7864 (tt0) cc_final: 0.7576 (tt0) REVERT: C 643 MET cc_start: 0.8942 (mtt) cc_final: 0.8691 (mtt) REVERT: C 666 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8265 (mm-30) outliers start: 12 outliers final: 7 residues processed: 294 average time/residue: 0.6374 time to fit residues: 213.4507 Evaluate side-chains 280 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 273 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 288 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 50 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 854 GLN D 854 GLN B 854 GLN C 854 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106400 restraints weight = 47486.924| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.74 r_work: 0.2982 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23864 Z= 0.119 Angle : 1.030 58.738 32388 Z= 0.399 Chirality : 0.038 0.194 3676 Planarity : 0.004 0.049 3992 Dihedral : 9.872 126.332 3388 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.27 % Allowed : 12.13 % Favored : 86.61 % 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: 0.12 (0.15), residues: 2908 helix: 0.90 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -1.86 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.017 0.001 TYR C 209 PHE 0.011 0.001 PHE D 537 TRP 0.020 0.001 TRP C 391 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23860) covalent geometry : angle 1.03021 / 0.40 (32380) SS BOND : bond 0.00306 / 0.14 ( 4) SS BOND : angle 0.07898 / 0.05 ( 8) hydrogen bonds : bond 0.04247 / 2.90 ( 1340) hydrogen bonds : angle 3.21755 / 2.32 ( 3980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.861 Fit side-chains REVERT: A 131 TYR cc_start: 0.8444 (p90) cc_final: 0.8034 (p90) REVERT: A 407 PHE cc_start: 0.7248 (t80) cc_final: 0.6751 (m-80) REVERT: A 441 MET cc_start: 0.8607 (mmm) cc_final: 0.8354 (mmm) REVERT: A 494 MET cc_start: 0.7767 (mtt) cc_final: 0.7549 (mmm) REVERT: A 524 GLU cc_start: 0.7768 (tt0) cc_final: 0.7503 (tt0) REVERT: A 643 MET cc_start: 0.8812 (mtt) cc_final: 0.8560 (mtt) REVERT: A 666 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 859 MET cc_start: 0.8813 (mmm) cc_final: 0.8537 (mmm) REVERT: D 131 TYR cc_start: 0.8455 (p90) cc_final: 0.8040 (p90) REVERT: D 407 PHE cc_start: 0.7252 (t80) cc_final: 0.6745 (m-80) REVERT: D 441 MET cc_start: 0.8615 (mmm) cc_final: 0.8364 (mmm) REVERT: D 494 MET cc_start: 0.7758 (mtt) cc_final: 0.7531 (mmm) REVERT: D 524 GLU cc_start: 0.7760 (tt0) cc_final: 0.7491 (tt0) REVERT: D 643 MET cc_start: 0.8819 (mtt) cc_final: 0.8567 (mtt) REVERT: D 666 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8016 (mm-30) REVERT: D 859 MET cc_start: 0.8793 (mmm) cc_final: 0.8481 (mmm) REVERT: B 131 TYR cc_start: 0.8433 (p90) cc_final: 0.8035 (p90) REVERT: B 407 PHE cc_start: 0.7253 (t80) cc_final: 0.6761 (m-80) REVERT: B 441 MET cc_start: 0.8606 (mmm) cc_final: 0.8355 (mmm) REVERT: B 494 MET cc_start: 0.7776 (mtt) cc_final: 0.7556 (mmm) REVERT: B 524 GLU cc_start: 0.7766 (tt0) cc_final: 0.7500 (tt0) REVERT: B 643 MET cc_start: 0.8814 (mtt) cc_final: 0.8561 (mtt) REVERT: B 666 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8020 (mm-30) REVERT: B 859 MET cc_start: 0.8812 (mmm) cc_final: 0.8541 (mmm) REVERT: C 131 TYR cc_start: 0.8440 (p90) cc_final: 0.8040 (p90) REVERT: C 407 PHE cc_start: 0.7304 (t80) cc_final: 0.6801 (m-80) REVERT: C 441 MET cc_start: 0.8619 (mmm) cc_final: 0.8364 (mmm) REVERT: C 494 MET cc_start: 0.7755 (mtt) cc_final: 0.7532 (mmm) REVERT: C 524 GLU cc_start: 0.7757 (tt0) cc_final: 0.7490 (tt0) REVERT: C 643 MET cc_start: 0.8819 (mtt) cc_final: 0.8560 (mtt) REVERT: C 666 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8073 (mm-30) REVERT: C 859 MET cc_start: 0.8803 (mmm) cc_final: 0.8530 (mmm) outliers start: 29 outliers final: 3 residues processed: 284 average time/residue: 0.6598 time to fit residues: 213.7946 Evaluate side-chains 265 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 262 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain C residue 104 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 187 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100984 restraints weight = 44009.218| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.49 r_work: 0.2921 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23864 Z= 0.210 Angle : 1.082 58.309 32388 Z= 0.433 Chirality : 0.043 0.262 3676 Planarity : 0.005 0.049 3992 Dihedral : 10.115 127.804 3388 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.05 % Allowed : 12.91 % Favored : 86.04 % 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: 0.29 (0.16), residues: 2908 helix: 0.97 (0.11), residues: 2052 sheet: None (None), residues: 0 loop : -1.69 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 365 TYR 0.030 0.002 TYR C 209 PHE 0.017 0.002 PHE D 537 TRP 0.027 0.002 TRP D 391 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 (23860) covalent geometry : angle 1.08233 / 0.43 (32380) SS BOND : bond 0.00595 / 0.27 ( 4) SS BOND : angle 0.54623 / 0.32 ( 8) hydrogen bonds : bond 0.05560 / 3.80 ( 1340) hydrogen bonds : angle 3.36405 / 2.43 ( 3980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 302 time to evaluate : 0.807 Fit side-chains REVERT: A 407 PHE cc_start: 0.7210 (t80) cc_final: 0.6663 (m-80) REVERT: A 441 MET cc_start: 0.8842 (mmm) cc_final: 0.8595 (mmm) REVERT: A 530 ASP cc_start: 0.7968 (m-30) cc_final: 0.7730 (m-30) REVERT: A 643 MET cc_start: 0.8983 (mtt) cc_final: 0.8718 (mtt) REVERT: A 666 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 859 MET cc_start: 0.9019 (mmm) cc_final: 0.8778 (mmm) REVERT: D 407 PHE cc_start: 0.7203 (t80) cc_final: 0.6649 (m-80) REVERT: D 441 MET cc_start: 0.8843 (mmm) cc_final: 0.8597 (mmm) REVERT: D 530 ASP cc_start: 0.7971 (m-30) cc_final: 0.7698 (m-30) REVERT: D 643 MET cc_start: 0.8992 (mtt) cc_final: 0.8726 (mtt) REVERT: D 666 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8345 (mm-30) REVERT: D 859 MET cc_start: 0.9040 (mmm) cc_final: 0.8797 (mmm) REVERT: B 407 PHE cc_start: 0.7217 (t80) cc_final: 0.6674 (m-80) REVERT: B 441 MET cc_start: 0.8838 (mmm) cc_final: 0.8593 (mmm) REVERT: B 530 ASP cc_start: 0.7971 (m-30) cc_final: 0.7736 (m-30) REVERT: B 643 MET cc_start: 0.8984 (mtt) cc_final: 0.8719 (mtt) REVERT: B 666 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8355 (mm-30) REVERT: B 859 MET cc_start: 0.9035 (mmm) cc_final: 0.8799 (mmm) REVERT: C 131 TYR cc_start: 0.8485 (p90) cc_final: 0.8195 (p90) REVERT: C 407 PHE cc_start: 0.7325 (t80) cc_final: 0.6652 (m-80) REVERT: C 441 MET cc_start: 0.8850 (mmm) cc_final: 0.8601 (mmm) REVERT: C 530 ASP cc_start: 0.7989 (m-30) cc_final: 0.7755 (m-30) REVERT: C 643 MET cc_start: 0.8990 (mtt) cc_final: 0.8729 (mtt) REVERT: C 666 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8354 (mm-30) REVERT: C 859 MET cc_start: 0.9031 (mmm) cc_final: 0.8799 (mmm) outliers start: 24 outliers final: 11 residues processed: 307 average time/residue: 0.6422 time to fit residues: 225.4334 Evaluate side-chains 296 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 285 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 546 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 250 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106077 restraints weight = 36230.634| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.07 r_work: 0.2981 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23864 Z= 0.118 Angle : 1.027 58.521 32388 Z= 0.397 Chirality : 0.038 0.159 3676 Planarity : 0.004 0.047 3992 Dihedral : 9.581 125.499 3388 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.83 % Allowed : 14.14 % Favored : 85.03 % 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: 0.88 (0.16), residues: 2908 helix: 1.43 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.014 0.001 TYR C 209 PHE 0.015 0.001 PHE D 548 TRP 0.016 0.001 TRP A 391 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23860) covalent geometry : angle 1.02706 / 0.40 (32380) SS BOND : bond 0.00295 / 0.14 ( 4) SS BOND : angle 0.06989 / 0.04 ( 8) hydrogen bonds : bond 0.04156 / 2.84 ( 1340) hydrogen bonds : angle 3.13377 / 2.25 ( 3980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 1.081 Fit side-chains REVERT: A 407 PHE cc_start: 0.7153 (t80) cc_final: 0.6720 (m-80) REVERT: A 441 MET cc_start: 0.8767 (mmm) cc_final: 0.8501 (mmm) REVERT: A 584 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.7932 (mt) REVERT: A 643 MET cc_start: 0.8938 (mtt) cc_final: 0.8658 (mtt) REVERT: A 666 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 859 MET cc_start: 0.8945 (mmm) cc_final: 0.8639 (mmm) REVERT: A 874 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8394 (ttmt) REVERT: D 407 PHE cc_start: 0.7155 (t80) cc_final: 0.6717 (m-80) REVERT: D 441 MET cc_start: 0.8767 (mmm) cc_final: 0.8501 (mmm) REVERT: D 584 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.7904 (mt) REVERT: D 643 MET cc_start: 0.8936 (mtt) cc_final: 0.8656 (mtt) REVERT: D 666 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 859 MET cc_start: 0.8952 (mmm) cc_final: 0.8626 (mmm) REVERT: D 874 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8400 (ttmt) REVERT: B 407 PHE cc_start: 0.7152 (t80) cc_final: 0.6724 (m-80) REVERT: B 441 MET cc_start: 0.8764 (mmm) cc_final: 0.8498 (mmm) REVERT: B 584 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.7923 (mt) REVERT: B 643 MET cc_start: 0.8936 (mtt) cc_final: 0.8654 (mtt) REVERT: B 666 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 859 MET cc_start: 0.8970 (mmm) cc_final: 0.8667 (mmm) REVERT: B 874 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8390 (ttmt) REVERT: C 407 PHE cc_start: 0.7138 (t80) cc_final: 0.6720 (m-80) REVERT: C 441 MET cc_start: 0.8767 (mmm) cc_final: 0.8501 (mmm) REVERT: C 584 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.7943 (mt) REVERT: C 643 MET cc_start: 0.8935 (mtt) cc_final: 0.8656 (mtt) REVERT: C 666 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8226 (mm-30) REVERT: C 859 MET cc_start: 0.8966 (mmm) cc_final: 0.8666 (mmm) REVERT: C 874 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8422 (ttmt) outliers start: 19 outliers final: 4 residues processed: 303 average time/residue: 0.6195 time to fit residues: 215.6055 Evaluate side-chains 293 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 285 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106170 restraints weight = 51478.665| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.26 r_work: 0.2931 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23864 Z= 0.117 Angle : 1.022 58.431 32388 Z= 0.394 Chirality : 0.038 0.161 3676 Planarity : 0.004 0.046 3992 Dihedral : 8.857 124.971 3388 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.92 % Allowed : 14.40 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.16), residues: 2908 helix: 1.69 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 437 TYR 0.014 0.001 TYR A 209 PHE 0.009 0.001 PHE C 419 TRP 0.017 0.001 TRP A 391 HIS 0.002 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23860) covalent geometry : angle 1.02197 / 0.39 (32380) SS BOND : bond 0.00274 / 0.13 ( 4) SS BOND : angle 0.07813 / 0.05 ( 8) hydrogen bonds : bond 0.03977 / 2.72 ( 1340) hydrogen bonds : angle 3.03442 / 2.17 ( 3980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.829 Fit side-chains REVERT: A 259 ASN cc_start: 0.8084 (m-40) cc_final: 0.7430 (p0) REVERT: A 407 PHE cc_start: 0.7058 (t80) cc_final: 0.6664 (m-80) REVERT: A 441 MET cc_start: 0.8663 (mmm) cc_final: 0.8400 (mmm) REVERT: A 584 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 643 MET cc_start: 0.8839 (mtt) cc_final: 0.8603 (mtt) REVERT: A 666 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 859 MET cc_start: 0.8910 (mmm) cc_final: 0.8602 (mmm) REVERT: A 874 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8313 (ttmt) REVERT: D 259 ASN cc_start: 0.8092 (m-40) cc_final: 0.7437 (p0) REVERT: D 407 PHE cc_start: 0.7055 (t80) cc_final: 0.6655 (m-80) REVERT: D 441 MET cc_start: 0.8671 (mmm) cc_final: 0.8410 (mmm) REVERT: D 584 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8107 (mt) REVERT: D 643 MET cc_start: 0.8835 (mtt) cc_final: 0.8595 (mtt) REVERT: D 666 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8061 (mm-30) REVERT: D 859 MET cc_start: 0.8900 (mmm) cc_final: 0.8570 (mmm) REVERT: D 874 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8316 (ttmt) REVERT: B 259 ASN cc_start: 0.8084 (m-40) cc_final: 0.7434 (p0) REVERT: B 407 PHE cc_start: 0.7055 (t80) cc_final: 0.6667 (m-80) REVERT: B 441 MET cc_start: 0.8665 (mmm) cc_final: 0.8403 (mmm) REVERT: B 584 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8105 (mt) REVERT: B 643 MET cc_start: 0.8831 (mtt) cc_final: 0.8592 (mtt) REVERT: B 666 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 859 MET cc_start: 0.8920 (mmm) cc_final: 0.8615 (mmm) REVERT: B 874 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8315 (ttmt) REVERT: C 259 ASN cc_start: 0.7937 (m-40) cc_final: 0.7345 (p0) REVERT: C 407 PHE cc_start: 0.7043 (t80) cc_final: 0.6660 (m-80) REVERT: C 441 MET cc_start: 0.8661 (mmm) cc_final: 0.8398 (mmm) REVERT: C 584 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8114 (mt) REVERT: C 643 MET cc_start: 0.8836 (mtt) cc_final: 0.8598 (mtt) REVERT: C 666 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 859 MET cc_start: 0.8909 (mmm) cc_final: 0.8605 (mmm) REVERT: C 874 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8258 (ttmt) outliers start: 21 outliers final: 7 residues processed: 296 average time/residue: 0.6103 time to fit residues: 208.0269 Evaluate side-chains 294 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 283 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 691 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106364 restraints weight = 42152.612| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.30 r_work: 0.2986 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23864 Z= 0.118 Angle : 1.024 58.422 32388 Z= 0.395 Chirality : 0.038 0.157 3676 Planarity : 0.004 0.044 3992 Dihedral : 8.510 124.203 3388 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.05 % Allowed : 14.49 % Favored : 84.47 % 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: 1.37 (0.16), residues: 2908 helix: 1.82 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.37 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.014 0.001 TYR B 209 PHE 0.018 0.001 PHE C 548 TRP 0.017 0.001 TRP D 391 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23860) covalent geometry : angle 1.02446 / 0.39 (32380) SS BOND : bond 0.00306 / 0.14 ( 4) SS BOND : angle 0.13032 / 0.08 ( 8) hydrogen bonds : bond 0.03945 / 2.69 ( 1340) hydrogen bonds : angle 3.00130 / 2.14 ( 3980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.964 Fit side-chains REVERT: A 259 ASN cc_start: 0.8028 (m-40) cc_final: 0.7446 (p0) REVERT: A 407 PHE cc_start: 0.7111 (t80) cc_final: 0.6736 (m-80) REVERT: A 441 MET cc_start: 0.8807 (mmm) cc_final: 0.8540 (mmm) REVERT: A 511 LYS cc_start: 0.7502 (ttmm) cc_final: 0.7287 (ttmt) REVERT: A 584 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 643 MET cc_start: 0.8977 (mtt) cc_final: 0.8765 (mtt) REVERT: A 666 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8247 (mm-30) REVERT: A 859 MET cc_start: 0.9004 (mmm) cc_final: 0.8731 (mmm) REVERT: A 874 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8436 (ttmt) REVERT: D 259 ASN cc_start: 0.8039 (m-40) cc_final: 0.7459 (p0) REVERT: D 407 PHE cc_start: 0.7123 (t80) cc_final: 0.6742 (m-80) REVERT: D 441 MET cc_start: 0.8820 (mmm) cc_final: 0.8555 (mmm) REVERT: D 511 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7309 (ttmt) REVERT: D 584 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8236 (mt) REVERT: D 643 MET cc_start: 0.8979 (mtt) cc_final: 0.8768 (mtt) REVERT: D 666 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8265 (mm-30) REVERT: D 859 MET cc_start: 0.9008 (mmm) cc_final: 0.8721 (mmm) REVERT: D 874 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8437 (ttmt) REVERT: B 259 ASN cc_start: 0.8030 (m-40) cc_final: 0.7453 (p0) REVERT: B 407 PHE cc_start: 0.7116 (t80) cc_final: 0.6750 (m-80) REVERT: B 441 MET cc_start: 0.8819 (mmm) cc_final: 0.8552 (mmm) REVERT: B 511 LYS cc_start: 0.7494 (ttmm) cc_final: 0.7288 (ttmt) REVERT: B 584 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 643 MET cc_start: 0.8984 (mtt) cc_final: 0.8775 (mtt) REVERT: B 666 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8252 (mm-30) REVERT: B 859 MET cc_start: 0.9013 (mmm) cc_final: 0.8742 (mmm) REVERT: B 874 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8446 (ttmt) REVERT: C 259 ASN cc_start: 0.7979 (m-40) cc_final: 0.7437 (p0) REVERT: C 407 PHE cc_start: 0.7108 (t80) cc_final: 0.6744 (m-80) REVERT: C 441 MET cc_start: 0.8821 (mmm) cc_final: 0.8556 (mmm) REVERT: C 511 LYS cc_start: 0.7498 (ttmm) cc_final: 0.7290 (ttmt) REVERT: C 584 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8231 (mt) REVERT: C 643 MET cc_start: 0.8982 (mtt) cc_final: 0.8771 (mtt) REVERT: C 666 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8251 (mm-30) REVERT: C 859 MET cc_start: 0.8999 (mmm) cc_final: 0.8724 (mmm) REVERT: C 874 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8477 (ttmm) outliers start: 24 outliers final: 16 residues processed: 307 average time/residue: 0.5976 time to fit residues: 211.4277 Evaluate side-chains 311 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 132 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 284 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106945 restraints weight = 40000.914| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.25 r_work: 0.3001 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23864 Z= 0.112 Angle : 1.016 58.414 32388 Z= 0.390 Chirality : 0.038 0.158 3676 Planarity : 0.004 0.044 3992 Dihedral : 8.164 123.603 3388 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.92 % Allowed : 15.31 % Favored : 83.77 % 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: 1.51 (0.16), residues: 2908 helix: 1.92 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.014 0.001 TYR B 209 PHE 0.011 0.001 PHE D 419 TRP 0.016 0.001 TRP A 391 HIS 0.002 0.001 HIS D 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (23860) covalent geometry : angle 1.01648 / 0.39 (32380) SS BOND : bond 0.00274 / 0.13 ( 4) SS BOND : angle 0.10045 / 0.06 ( 8) hydrogen bonds : bond 0.03818 / 2.61 ( 1340) hydrogen bonds : angle 2.95839 / 2.11 ( 3980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 289 time to evaluate : 0.882 Fit side-chains REVERT: A 259 ASN cc_start: 0.8003 (m-40) cc_final: 0.7424 (p0) REVERT: A 407 PHE cc_start: 0.7061 (t80) cc_final: 0.6709 (m-80) REVERT: A 441 MET cc_start: 0.8786 (mmm) cc_final: 0.8468 (mmm) REVERT: A 584 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 643 MET cc_start: 0.8954 (mtt) cc_final: 0.8629 (mtt) REVERT: A 666 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 874 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8443 (ttmt) REVERT: D 259 ASN cc_start: 0.8005 (m-40) cc_final: 0.7436 (p0) REVERT: D 407 PHE cc_start: 0.7063 (t80) cc_final: 0.6711 (m-80) REVERT: D 441 MET cc_start: 0.8789 (mmm) cc_final: 0.8471 (mmm) REVERT: D 584 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 643 MET cc_start: 0.8950 (mtt) cc_final: 0.8624 (mtt) REVERT: D 666 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 874 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8448 (ttmt) REVERT: B 259 ASN cc_start: 0.8016 (m-40) cc_final: 0.7439 (p0) REVERT: B 407 PHE cc_start: 0.7061 (t80) cc_final: 0.6723 (m-80) REVERT: B 441 MET cc_start: 0.8795 (mmm) cc_final: 0.8477 (mmm) REVERT: B 584 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 643 MET cc_start: 0.8957 (mtt) cc_final: 0.8637 (mtt) REVERT: B 666 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 859 MET cc_start: 0.8993 (mmm) cc_final: 0.8723 (mmm) REVERT: B 874 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8450 (ttmt) REVERT: C 259 ASN cc_start: 0.7960 (m-40) cc_final: 0.7420 (p0) REVERT: C 407 PHE cc_start: 0.7056 (t80) cc_final: 0.6717 (m-80) REVERT: C 441 MET cc_start: 0.8796 (mmm) cc_final: 0.8479 (mmm) REVERT: C 584 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8181 (mt) REVERT: C 643 MET cc_start: 0.8959 (mtt) cc_final: 0.8640 (mtt) REVERT: C 666 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8226 (mm-30) REVERT: C 859 MET cc_start: 0.9008 (mmm) cc_final: 0.8742 (mmm) REVERT: C 874 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8471 (ttmm) outliers start: 21 outliers final: 15 residues processed: 299 average time/residue: 0.6191 time to fit residues: 212.9039 Evaluate side-chains 302 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 6 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 GLN D 856 GLN B 856 GLN C 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104335 restraints weight = 44420.474| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.61 r_work: 0.2926 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23864 Z= 0.174 Angle : 1.061 58.287 32388 Z= 0.416 Chirality : 0.041 0.219 3676 Planarity : 0.004 0.045 3992 Dihedral : 8.247 124.583 3388 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.31 % Allowed : 15.05 % Favored : 83.64 % 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: 1.23 (0.16), residues: 2908 helix: 1.70 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.39 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 437 TYR 0.024 0.002 TYR C 209 PHE 0.020 0.002 PHE A 548 TRP 0.024 0.002 TRP B 391 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.17 (23860) covalent geometry : angle 1.06154 / 0.42 (32380) SS BOND : bond 0.00493 / 0.23 ( 4) SS BOND : angle 0.44148 / 0.26 ( 8) hydrogen bonds : bond 0.04898 / 3.35 ( 1340) hydrogen bonds : angle 3.12362 / 2.24 ( 3980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.905 Fit side-chains REVERT: A 259 ASN cc_start: 0.7926 (m-40) cc_final: 0.7427 (p0) REVERT: A 407 PHE cc_start: 0.7125 (t80) cc_final: 0.6733 (m-80) REVERT: A 511 LYS cc_start: 0.7271 (ttmm) cc_final: 0.7044 (ttmt) REVERT: A 530 ASP cc_start: 0.7850 (m-30) cc_final: 0.7275 (m-30) REVERT: A 584 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 643 MET cc_start: 0.8841 (mtt) cc_final: 0.8555 (mtt) REVERT: A 666 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 874 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8306 (ttmt) REVERT: D 259 ASN cc_start: 0.7934 (m-40) cc_final: 0.7427 (p0) REVERT: D 407 PHE cc_start: 0.7126 (t80) cc_final: 0.6735 (m-80) REVERT: D 511 LYS cc_start: 0.7280 (ttmm) cc_final: 0.7054 (ttmt) REVERT: D 530 ASP cc_start: 0.7852 (m-30) cc_final: 0.7275 (m-30) REVERT: D 584 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8267 (mt) REVERT: D 643 MET cc_start: 0.8850 (mtt) cc_final: 0.8541 (mtt) REVERT: D 666 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7960 (mm-30) REVERT: D 874 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8309 (ttmt) REVERT: B 259 ASN cc_start: 0.7925 (m-40) cc_final: 0.7428 (p0) REVERT: B 407 PHE cc_start: 0.7127 (t80) cc_final: 0.6744 (m-80) REVERT: B 511 LYS cc_start: 0.7265 (ttmm) cc_final: 0.7038 (ttmt) REVERT: B 530 ASP cc_start: 0.7849 (m-30) cc_final: 0.7272 (m-30) REVERT: B 584 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 643 MET cc_start: 0.8836 (mtt) cc_final: 0.8547 (mtt) REVERT: B 666 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 874 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8302 (ttmt) REVERT: C 259 ASN cc_start: 0.7922 (m-40) cc_final: 0.7446 (p0) REVERT: C 407 PHE cc_start: 0.7121 (t80) cc_final: 0.6741 (m-80) REVERT: C 511 LYS cc_start: 0.7263 (ttmm) cc_final: 0.7037 (ttmt) REVERT: C 530 ASP cc_start: 0.7854 (m-30) cc_final: 0.7284 (m-30) REVERT: C 584 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8266 (mt) REVERT: C 643 MET cc_start: 0.8844 (mtt) cc_final: 0.8557 (mtt) REVERT: C 666 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7958 (mm-30) REVERT: C 874 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8356 (ttmm) outliers start: 30 outliers final: 16 residues processed: 317 average time/residue: 0.6112 time to fit residues: 222.6012 Evaluate side-chains 315 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 4 optimal weight: 0.0470 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 8.9990 chunk 273 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108636 restraints weight = 35620.295| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.02 r_work: 0.3034 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23864 Z= 0.108 Angle : 1.029 58.445 32388 Z= 0.395 Chirality : 0.037 0.141 3676 Planarity : 0.004 0.045 3992 Dihedral : 7.841 122.622 3388 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.74 % Allowed : 15.97 % Favored : 83.29 % 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: 1.67 (0.16), residues: 2908 helix: 2.04 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 437 TYR 0.012 0.001 TYR A 708 PHE 0.012 0.001 PHE D 419 TRP 0.015 0.001 TRP A 391 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (23860) covalent geometry : angle 1.02949 / 0.39 (32380) SS BOND : bond 0.00240 / 0.11 ( 4) SS BOND : angle 0.07530 / 0.04 ( 8) hydrogen bonds : bond 0.03733 / 2.55 ( 1340) hydrogen bonds : angle 2.96493 / 2.12 ( 3980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.852 Fit side-chains REVERT: A 259 ASN cc_start: 0.7988 (m-40) cc_final: 0.7426 (p0) REVERT: A 407 PHE cc_start: 0.7082 (t80) cc_final: 0.6714 (m-80) REVERT: A 511 LYS cc_start: 0.7247 (ttmm) cc_final: 0.7013 (ttmt) REVERT: A 584 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8270 (mt) REVERT: A 643 MET cc_start: 0.8914 (mtt) cc_final: 0.8677 (mtt) REVERT: A 666 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 874 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8419 (ttmt) REVERT: D 259 ASN cc_start: 0.7995 (m-40) cc_final: 0.7439 (p0) REVERT: D 407 PHE cc_start: 0.7085 (t80) cc_final: 0.6714 (m-80) REVERT: D 511 LYS cc_start: 0.7261 (ttmm) cc_final: 0.7027 (ttmt) REVERT: D 584 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (mt) REVERT: D 643 MET cc_start: 0.8919 (mtt) cc_final: 0.8679 (mtt) REVERT: D 666 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8091 (mm-30) REVERT: D 874 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8419 (ttmt) REVERT: B 259 ASN cc_start: 0.7990 (m-40) cc_final: 0.7427 (p0) REVERT: B 407 PHE cc_start: 0.7089 (t80) cc_final: 0.6729 (m-80) REVERT: B 511 LYS cc_start: 0.7229 (ttmm) cc_final: 0.6996 (ttmt) REVERT: B 584 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 643 MET cc_start: 0.8922 (mtt) cc_final: 0.8686 (mtt) REVERT: B 666 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8098 (mm-30) REVERT: B 874 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8413 (ttmt) REVERT: C 259 ASN cc_start: 0.7937 (m-40) cc_final: 0.7413 (p0) REVERT: C 407 PHE cc_start: 0.7078 (t80) cc_final: 0.6722 (m-80) REVERT: C 511 LYS cc_start: 0.7251 (ttmm) cc_final: 0.7014 (ttmt) REVERT: C 584 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 643 MET cc_start: 0.8924 (mtt) cc_final: 0.8689 (mtt) REVERT: C 666 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8075 (mm-30) REVERT: C 874 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8443 (ttmm) outliers start: 17 outliers final: 9 residues processed: 301 average time/residue: 0.6231 time to fit residues: 215.4938 Evaluate side-chains 302 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 289 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 878 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 284 optimal weight: 0.0020 chunk 87 optimal weight: 0.6980 chunk 262 optimal weight: 0.0670 chunk 206 optimal weight: 5.9990 chunk 116 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 223 optimal weight: 0.0010 chunk 122 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113535 restraints weight = 42217.816| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.29 r_work: 0.3091 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23864 Z= 0.094 Angle : 1.015 58.292 32388 Z= 0.384 Chirality : 0.036 0.150 3676 Planarity : 0.004 0.045 3992 Dihedral : 7.305 121.324 3388 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.22 % Allowed : 16.54 % Favored : 83.25 % 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: 2.08 (0.16), residues: 2908 helix: 2.33 (0.12), residues: 2060 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 437 TYR 0.014 0.001 TYR A 708 PHE 0.012 0.001 PHE A 419 TRP 0.015 0.001 TRP A 680 HIS 0.001 0.000 HIS B 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (23860) covalent geometry : angle 1.01485 / 0.38 (32380) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.16594 / 0.10 ( 8) hydrogen bonds : bond 0.02790 / 1.90 ( 1340) hydrogen bonds : angle 2.79824 / 1.98 ( 3980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8083.48 seconds wall clock time: 138 minutes 4.75 seconds (8284.75 seconds total)