Starting phenix.real_space_refine on Thu Mar 5 16:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uz8_20953/03_2026/6uz8_20953.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz8_20953/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uz8_20953/03_2026/6uz8_20953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz8_20953/03_2026/6uz8_20953.map" model { file = "/net/cci-nas-00/data/ceres_data/6uz8_20953/03_2026/6uz8_20953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz8_20953/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 10.05, per 1000 atoms: 0.43 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: 1.79 Conformation dependent library (CDL) restraints added in 1.6 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: 0.62 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: 4.16 Time building geometry restraints manager: 2.46 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: 14308 35.90 - 71.80: 284 71.80 - 107.71: 20 107.71 - 143.61: 0 143.61 - 179.51: 4 Dihedral angle restraints: 14616 sinusoidal: 5956 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 14613 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 C1001 " 0.007 2.00e-02 2.50e+03 4.61e-02 5.32e+01 pdb=" C03 R0D C1001 " 0.010 2.00e-02 2.50e+03 pdb=" C04 R0D C1001 " -0.005 2.00e-02 2.50e+03 pdb=" C05 R0D C1001 " -0.025 2.00e-02 2.50e+03 pdb=" C07 R0D C1001 " 0.118 2.00e-02 2.50e+03 pdb=" C08 R0D C1001 " -0.055 2.00e-02 2.50e+03 pdb=" C26 R0D C1001 " -0.026 2.00e-02 2.50e+03 pdb=" C27 R0D C1001 " -0.012 2.00e-02 2.50e+03 pdb=" N06 R0D C1001 " -0.042 2.00e-02 2.50e+03 pdb="CL01 R0D C1001 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D B1001 " 0.007 2.00e-02 2.50e+03 4.61e-02 5.32e+01 pdb=" C03 R0D B1001 " 0.010 2.00e-02 2.50e+03 pdb=" C04 R0D B1001 " -0.005 2.00e-02 2.50e+03 pdb=" C05 R0D B1001 " -0.025 2.00e-02 2.50e+03 pdb=" C07 R0D B1001 " 0.118 2.00e-02 2.50e+03 pdb=" C08 R0D B1001 " -0.055 2.00e-02 2.50e+03 pdb=" C26 R0D B1001 " -0.026 2.00e-02 2.50e+03 pdb=" C27 R0D B1001 " -0.012 2.00e-02 2.50e+03 pdb=" N06 R0D B1001 " -0.042 2.00e-02 2.50e+03 pdb="CL01 R0D B1001 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 R0D D1003 " -0.007 2.00e-02 2.50e+03 4.60e-02 5.30e+01 pdb=" C03 R0D D1003 " -0.011 2.00e-02 2.50e+03 pdb=" C04 R0D D1003 " 0.005 2.00e-02 2.50e+03 pdb=" C05 R0D D1003 " 0.025 2.00e-02 2.50e+03 pdb=" C07 R0D D1003 " -0.118 2.00e-02 2.50e+03 pdb=" C08 R0D D1003 " 0.055 2.00e-02 2.50e+03 pdb=" C26 R0D D1003 " 0.026 2.00e-02 2.50e+03 pdb=" C27 R0D D1003 " 0.012 2.00e-02 2.50e+03 pdb=" N06 R0D D1003 " 0.042 2.00e-02 2.50e+03 pdb="CL01 R0D D1003 " -0.029 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: 0.04 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.160 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.007 0.074 3992 Dihedral : 14.599 179.509 8988 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 covalent geometry : bond 0.00795 (23860) covalent geometry : angle 1.04578 (32380) SS BOND : bond 0.00657 ( 4) SS BOND : angle 0.61085 ( 8) hydrogen bonds : bond 0.13729 ( 1340) hydrogen bonds : angle 5.50010 ( 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 : 0.968 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: 0.7109 time to fit residues: 320.1247 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 : 0.745 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3696 r_free = 0.3696 target = 0.145822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106561 restraints weight = 57458.430| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.58 r_work: 0.3017 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 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 = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23864 Z= 0.111 Angle : 0.541 9.982 32388 Z= 0.281 Chirality : 0.037 0.122 3676 Planarity : 0.005 0.055 3992 Dihedral : 11.031 116.910 3960 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.70 % Allowed : 10.73 % Favored : 88.57 % 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: -1.08 (0.14), residues: 2908 helix: -0.01 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 101 TYR 0.016 0.001 TYR B 708 PHE 0.009 0.001 PHE D 537 TRP 0.016 0.001 TRP C 391 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00241 (23860) covalent geometry : angle 0.54130 (32380) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.19577 ( 8) hydrogen bonds : bond 0.04328 ( 1340) hydrogen bonds : angle 3.44482 ( 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 303 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 0.798 Fit side-chains REVERT: A 130 ASP cc_start: 0.8179 (t0) cc_final: 0.7976 (t0) REVERT: A 407 PHE cc_start: 0.7233 (t80) cc_final: 0.6584 (m-80) REVERT: A 441 MET cc_start: 0.8763 (mmm) cc_final: 0.8481 (mmm) REVERT: A 494 MET cc_start: 0.7917 (mtt) cc_final: 0.7672 (mmm) REVERT: A 524 GLU cc_start: 0.7831 (tt0) cc_final: 0.7578 (tt0) REVERT: A 643 MET cc_start: 0.8927 (mtt) cc_final: 0.8680 (mtt) REVERT: A 666 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8247 (mm-30) REVERT: D 130 ASP cc_start: 0.8315 (t0) cc_final: 0.8082 (t0) REVERT: D 407 PHE cc_start: 0.7235 (t80) cc_final: 0.6573 (m-80) REVERT: D 441 MET cc_start: 0.8756 (mmm) cc_final: 0.8478 (mmm) REVERT: D 494 MET cc_start: 0.7907 (mtt) cc_final: 0.7661 (mmm) REVERT: D 524 GLU cc_start: 0.7827 (tt0) cc_final: 0.7575 (tt0) REVERT: D 643 MET cc_start: 0.8934 (mtt) cc_final: 0.8686 (mtt) REVERT: D 666 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8260 (mm-30) REVERT: B 130 ASP cc_start: 0.8166 (t0) cc_final: 0.7954 (t0) REVERT: B 407 PHE cc_start: 0.7245 (t80) cc_final: 0.6592 (m-80) REVERT: B 441 MET cc_start: 0.8758 (mmm) cc_final: 0.8481 (mmm) REVERT: B 494 MET cc_start: 0.7927 (mtt) cc_final: 0.7686 (mmm) REVERT: B 524 GLU cc_start: 0.7821 (tt0) cc_final: 0.7571 (tt0) REVERT: B 643 MET cc_start: 0.8909 (mtt) cc_final: 0.8657 (mtt) REVERT: B 666 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8243 (mm-30) REVERT: C 130 ASP cc_start: 0.8236 (t0) cc_final: 0.8010 (t0) REVERT: C 407 PHE cc_start: 0.7220 (t80) cc_final: 0.6581 (m-80) REVERT: C 441 MET cc_start: 0.8764 (mmm) cc_final: 0.8485 (mmm) REVERT: C 494 MET cc_start: 0.7898 (mtt) cc_final: 0.7657 (mmm) REVERT: C 524 GLU cc_start: 0.7837 (tt0) cc_final: 0.7590 (tt0) REVERT: C 643 MET cc_start: 0.8920 (mtt) cc_final: 0.8667 (mtt) REVERT: C 666 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8247 (mm-30) outliers start: 16 outliers final: 4 residues processed: 299 average time/residue: 0.6715 time to fit residues: 228.1711 Evaluate side-chains 275 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain D 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: 1.9990 chunk 215 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 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: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3669 r_free = 0.3669 target = 0.143607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105446 restraints weight = 47575.218| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.80 r_work: 0.2962 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 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 = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23864 Z= 0.126 Angle : 0.539 8.459 32388 Z= 0.274 Chirality : 0.039 0.139 3676 Planarity : 0.004 0.049 3992 Dihedral : 10.200 95.044 3948 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.70 % Allowed : 12.65 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.15), residues: 2908 helix: 0.95 (0.12), residues: 2024 sheet: None (None), residues: 0 loop : -1.84 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 437 TYR 0.018 0.002 TYR C 209 PHE 0.013 0.001 PHE D 537 TRP 0.021 0.001 TRP D 391 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00295 (23860) covalent geometry : angle 0.53941 (32380) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.11744 ( 8) hydrogen bonds : bond 0.04443 ( 1340) hydrogen bonds : angle 3.22877 ( 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 296 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.925 Fit side-chains REVERT: A 131 TYR cc_start: 0.8448 (p90) cc_final: 0.8009 (p90) REVERT: A 407 PHE cc_start: 0.7225 (t80) cc_final: 0.6726 (m-80) REVERT: A 441 MET cc_start: 0.8598 (mmm) cc_final: 0.8350 (mmm) REVERT: A 643 MET cc_start: 0.8791 (mtt) cc_final: 0.8527 (mtt) REVERT: A 666 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 859 MET cc_start: 0.8842 (mmm) cc_final: 0.8561 (mmm) REVERT: D 131 TYR cc_start: 0.8453 (p90) cc_final: 0.8008 (p90) REVERT: D 407 PHE cc_start: 0.7224 (t80) cc_final: 0.6705 (m-80) REVERT: D 441 MET cc_start: 0.8596 (mmm) cc_final: 0.8354 (mmm) REVERT: D 494 MET cc_start: 0.7733 (mtt) cc_final: 0.7524 (mmm) REVERT: D 643 MET cc_start: 0.8797 (mtt) cc_final: 0.8532 (mtt) REVERT: D 666 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 131 TYR cc_start: 0.8422 (p90) cc_final: 0.7961 (p90) REVERT: B 407 PHE cc_start: 0.7222 (t80) cc_final: 0.6715 (m-80) REVERT: B 441 MET cc_start: 0.8595 (mmm) cc_final: 0.8352 (mmm) REVERT: B 494 MET cc_start: 0.7738 (mtt) cc_final: 0.7538 (mmm) REVERT: B 530 ASP cc_start: 0.7764 (m-30) cc_final: 0.7548 (m-30) REVERT: B 643 MET cc_start: 0.8790 (mtt) cc_final: 0.8525 (mtt) REVERT: B 666 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 859 MET cc_start: 0.8846 (mmm) cc_final: 0.8568 (mmm) REVERT: C 131 TYR cc_start: 0.8453 (p90) cc_final: 0.8016 (p90) REVERT: C 407 PHE cc_start: 0.7211 (t80) cc_final: 0.6711 (m-80) REVERT: C 441 MET cc_start: 0.8602 (mmm) cc_final: 0.8355 (mmm) REVERT: C 524 GLU cc_start: 0.7753 (tt0) cc_final: 0.7482 (tt0) REVERT: C 530 ASP cc_start: 0.7773 (m-30) cc_final: 0.7559 (m-30) REVERT: C 643 MET cc_start: 0.8788 (mtt) cc_final: 0.8500 (mtt) REVERT: C 666 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 859 MET cc_start: 0.8842 (mmm) cc_final: 0.8562 (mmm) outliers start: 16 outliers final: 1 residues processed: 290 average time/residue: 0.7166 time to fit residues: 234.3877 Evaluate side-chains 268 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 283 optimal weight: 0.5980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3660 r_free = 0.3660 target = 0.143020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104626 restraints weight = 43778.012| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.47 r_work: 0.2980 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23864 Z= 0.125 Angle : 0.525 8.623 32388 Z= 0.271 Chirality : 0.039 0.152 3676 Planarity : 0.004 0.047 3992 Dihedral : 9.966 89.132 3948 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.05 % Allowed : 13.35 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2908 helix: 1.32 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.018 0.002 TYR D 209 PHE 0.017 0.001 PHE A 548 TRP 0.018 0.001 TRP D 391 HIS 0.002 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00294 (23860) covalent geometry : angle 0.52461 (32380) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.16080 ( 8) hydrogen bonds : bond 0.04241 ( 1340) hydrogen bonds : angle 3.12907 ( 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 312 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.901 Fit side-chains REVERT: A 407 PHE cc_start: 0.7262 (t80) cc_final: 0.6710 (m-80) REVERT: A 441 MET cc_start: 0.8789 (mmm) cc_final: 0.8534 (mmm) REVERT: A 459 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8266 (tpp) REVERT: A 643 MET cc_start: 0.8996 (mtt) cc_final: 0.8773 (mtt) REVERT: A 666 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8293 (mm-30) REVERT: A 859 MET cc_start: 0.8978 (mmm) cc_final: 0.8756 (mmm) REVERT: D 407 PHE cc_start: 0.7269 (t80) cc_final: 0.6712 (m-80) REVERT: D 441 MET cc_start: 0.8791 (mmm) cc_final: 0.8539 (mmm) REVERT: D 643 MET cc_start: 0.8996 (mtt) cc_final: 0.8764 (mtt) REVERT: D 666 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 407 PHE cc_start: 0.7273 (t80) cc_final: 0.6728 (m-80) REVERT: B 441 MET cc_start: 0.8789 (mmm) cc_final: 0.8537 (mmm) REVERT: B 643 MET cc_start: 0.8989 (mtt) cc_final: 0.8759 (mtt) REVERT: B 666 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 859 MET cc_start: 0.8991 (mmm) cc_final: 0.8670 (mmm) REVERT: C 407 PHE cc_start: 0.7248 (t80) cc_final: 0.6706 (m-80) REVERT: C 441 MET cc_start: 0.8795 (mmm) cc_final: 0.8540 (mmm) REVERT: C 643 MET cc_start: 0.8987 (mtt) cc_final: 0.8759 (mtt) REVERT: C 666 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 859 MET cc_start: 0.8994 (mmm) cc_final: 0.8773 (mmm) outliers start: 24 outliers final: 5 residues processed: 298 average time/residue: 0.6955 time to fit residues: 235.0939 Evaluate side-chains 275 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 269 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 435 ILE 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: 0.8980 chunk 238 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 225 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 chunk 250 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106761 restraints weight = 36212.371| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.14 r_work: 0.3014 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1897 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= 0.112 Angle : 0.507 8.967 32388 Z= 0.259 Chirality : 0.038 0.155 3676 Planarity : 0.004 0.045 3992 Dihedral : 9.648 88.892 3948 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.70 % Allowed : 14.83 % 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: 1.11 (0.16), residues: 2908 helix: 1.62 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.015 0.001 TYR C 209 PHE 0.009 0.001 PHE A 537 TRP 0.016 0.001 TRP D 391 HIS 0.002 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00258 (23860) covalent geometry : angle 0.50698 (32380) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.09745 ( 8) hydrogen bonds : bond 0.03957 ( 1340) hydrogen bonds : angle 3.03736 ( 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 300 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 0.879 Fit side-chains REVERT: A 259 ASN cc_start: 0.8128 (m-40) cc_final: 0.7489 (p0) REVERT: A 407 PHE cc_start: 0.7186 (t80) cc_final: 0.6745 (m-80) REVERT: A 441 MET cc_start: 0.8740 (mmm) cc_final: 0.8483 (mmm) REVERT: A 459 MET cc_start: 0.8501 (mmp) cc_final: 0.8274 (tpp) REVERT: A 643 MET cc_start: 0.8932 (mtt) cc_final: 0.8709 (mtt) REVERT: A 666 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 859 MET cc_start: 0.8951 (mmm) cc_final: 0.8658 (mmm) REVERT: A 874 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8406 (ttmt) REVERT: D 259 ASN cc_start: 0.8137 (m-40) cc_final: 0.7499 (p0) REVERT: D 407 PHE cc_start: 0.7187 (t80) cc_final: 0.6739 (m-80) REVERT: D 441 MET cc_start: 0.8737 (mmm) cc_final: 0.8479 (mmm) REVERT: D 643 MET cc_start: 0.8930 (mtt) cc_final: 0.8704 (mtt) REVERT: D 666 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 874 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8407 (ttmt) REVERT: B 259 ASN cc_start: 0.8132 (m-40) cc_final: 0.7492 (p0) REVERT: B 407 PHE cc_start: 0.7191 (t80) cc_final: 0.6753 (m-80) REVERT: B 441 MET cc_start: 0.8743 (mmm) cc_final: 0.8485 (mmm) REVERT: B 643 MET cc_start: 0.8930 (mtt) cc_final: 0.8706 (mtt) REVERT: B 666 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 859 MET cc_start: 0.8976 (mmm) cc_final: 0.8685 (mmm) REVERT: B 874 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8405 (ttmt) REVERT: C 259 ASN cc_start: 0.8116 (m-40) cc_final: 0.7481 (p0) REVERT: C 407 PHE cc_start: 0.7176 (t80) cc_final: 0.6745 (m-80) REVERT: C 441 MET cc_start: 0.8748 (mmm) cc_final: 0.8490 (mmm) REVERT: C 643 MET cc_start: 0.8923 (mtt) cc_final: 0.8695 (mtt) REVERT: C 666 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8201 (mm-30) REVERT: C 859 MET cc_start: 0.8968 (mmm) cc_final: 0.8673 (mmm) REVERT: C 874 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8401 (ttmt) outliers start: 16 outliers final: 8 residues processed: 288 average time/residue: 0.7043 time to fit residues: 230.7650 Evaluate side-chains 288 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 280 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain D residue 546 MET 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=3.00 ------------------------------------------------------------------------------- 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: 0.5980 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 120 optimal weight: 0.0050 chunk 72 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111151 restraints weight = 51196.766| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.28 r_work: 0.2989 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.002 0.036 23864 Z= 0.094 Angle : 0.485 8.618 32388 Z= 0.249 Chirality : 0.037 0.158 3676 Planarity : 0.004 0.045 3992 Dihedral : 9.088 88.225 3948 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.22 % Allowed : 15.40 % Favored : 84.38 % 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: 1.50 (0.16), residues: 2908 helix: 1.90 (0.12), residues: 2060 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 437 TYR 0.015 0.001 TYR C 708 PHE 0.018 0.001 PHE D 548 TRP 0.012 0.001 TRP B 391 HIS 0.001 0.000 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00202 (23860) covalent geometry : angle 0.48503 (32380) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.05773 ( 8) hydrogen bonds : bond 0.03351 ( 1340) hydrogen bonds : angle 2.90925 ( 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 296 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 0.770 Fit side-chains REVERT: A 259 ASN cc_start: 0.8115 (m-40) cc_final: 0.7507 (p0) REVERT: A 407 PHE cc_start: 0.7128 (t80) cc_final: 0.6778 (m-80) REVERT: A 441 MET cc_start: 0.8639 (mmm) cc_final: 0.8321 (mmm) REVERT: A 643 MET cc_start: 0.8813 (mtt) cc_final: 0.8445 (mtt) REVERT: A 666 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 853 ARG cc_start: 0.7125 (mpp80) cc_final: 0.6843 (mtm-85) REVERT: A 859 MET cc_start: 0.8864 (mmm) cc_final: 0.8587 (mmm) REVERT: A 874 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8362 (ttmt) REVERT: D 259 ASN cc_start: 0.8111 (m-40) cc_final: 0.7505 (p0) REVERT: D 407 PHE cc_start: 0.7123 (t80) cc_final: 0.6761 (m-80) REVERT: D 441 MET cc_start: 0.8633 (mmm) cc_final: 0.8385 (mmm) REVERT: D 643 MET cc_start: 0.8800 (mtt) cc_final: 0.8429 (mtt) REVERT: D 666 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 874 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8357 (ttmt) REVERT: B 259 ASN cc_start: 0.8117 (m-40) cc_final: 0.7517 (p0) REVERT: B 407 PHE cc_start: 0.7124 (t80) cc_final: 0.6775 (m-80) REVERT: B 441 MET cc_start: 0.8641 (mmm) cc_final: 0.8326 (mmm) REVERT: B 643 MET cc_start: 0.8815 (mtt) cc_final: 0.8450 (mtt) REVERT: B 666 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8039 (mm-30) REVERT: B 859 MET cc_start: 0.8869 (mmm) cc_final: 0.8574 (mmm) REVERT: B 874 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8356 (ttmt) REVERT: C 259 ASN cc_start: 0.7958 (m-40) cc_final: 0.7416 (p0) REVERT: C 407 PHE cc_start: 0.7109 (t80) cc_final: 0.6765 (m-80) REVERT: C 441 MET cc_start: 0.8644 (mmm) cc_final: 0.8329 (mmm) REVERT: C 643 MET cc_start: 0.8806 (mtt) cc_final: 0.8438 (mtt) REVERT: C 666 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 853 ARG cc_start: 0.7130 (mpp80) cc_final: 0.6871 (mtm-85) REVERT: C 859 MET cc_start: 0.8867 (mmm) cc_final: 0.8570 (mmm) REVERT: C 874 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8359 (ttmt) outliers start: 5 outliers final: 3 residues processed: 294 average time/residue: 0.6816 time to fit residues: 228.0378 Evaluate side-chains 289 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 435 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103580 restraints weight = 42339.402| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.33 r_work: 0.2942 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 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 = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23864 Z= 0.161 Angle : 0.559 9.533 32388 Z= 0.282 Chirality : 0.040 0.153 3676 Planarity : 0.004 0.044 3992 Dihedral : 9.283 89.396 3948 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.70 % Allowed : 15.58 % Favored : 83.73 % 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: 1.28 (0.16), residues: 2908 helix: 1.75 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 437 TYR 0.020 0.002 TYR C 209 PHE 0.013 0.001 PHE A 537 TRP 0.023 0.002 TRP A 391 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00398 (23860) covalent geometry : angle 0.55887 (32380) SS BOND : bond 0.00449 ( 4) SS BOND : angle 0.35590 ( 8) hydrogen bonds : bond 0.04676 ( 1340) hydrogen bonds : angle 3.07662 ( 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 321 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 305 time to evaluate : 0.877 Fit side-chains REVERT: A 259 ASN cc_start: 0.7973 (m-40) cc_final: 0.7439 (p0) REVERT: A 395 LEU cc_start: 0.8308 (pp) cc_final: 0.8107 (pp) REVERT: A 407 PHE cc_start: 0.7125 (t80) cc_final: 0.6828 (m-80) REVERT: A 441 MET cc_start: 0.8664 (mmm) cc_final: 0.8401 (mmm) REVERT: A 511 LYS cc_start: 0.7537 (ttmm) cc_final: 0.7327 (ttmt) REVERT: A 643 MET cc_start: 0.8849 (mtt) cc_final: 0.8528 (mtt) REVERT: A 666 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 853 ARG cc_start: 0.7217 (mpp80) cc_final: 0.6958 (mtm110) REVERT: A 874 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8307 (ttmt) REVERT: D 259 ASN cc_start: 0.7973 (m-40) cc_final: 0.7444 (p0) REVERT: D 407 PHE cc_start: 0.7126 (t80) cc_final: 0.6830 (m-80) REVERT: D 441 MET cc_start: 0.8623 (mmm) cc_final: 0.8379 (mmm) REVERT: D 511 LYS cc_start: 0.7547 (ttmm) cc_final: 0.7335 (ttmt) REVERT: D 643 MET cc_start: 0.8851 (mtt) cc_final: 0.8596 (mtt) REVERT: D 666 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 853 ARG cc_start: 0.7133 (mpp80) cc_final: 0.6891 (mtm110) REVERT: D 874 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8282 (ttmt) REVERT: B 259 ASN cc_start: 0.7972 (m-40) cc_final: 0.7442 (p0) REVERT: B 395 LEU cc_start: 0.8311 (pp) cc_final: 0.8103 (pp) REVERT: B 407 PHE cc_start: 0.7129 (t80) cc_final: 0.6837 (m-80) REVERT: B 441 MET cc_start: 0.8665 (mmm) cc_final: 0.8403 (mmm) REVERT: B 511 LYS cc_start: 0.7537 (ttmm) cc_final: 0.7325 (ttmt) REVERT: B 643 MET cc_start: 0.8841 (mtt) cc_final: 0.8519 (mtt) REVERT: B 666 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8039 (mm-30) REVERT: B 853 ARG cc_start: 0.7187 (mpp80) cc_final: 0.6952 (mtm110) REVERT: B 874 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8304 (ttmt) REVERT: C 259 ASN cc_start: 0.7960 (m-40) cc_final: 0.7434 (p0) REVERT: C 407 PHE cc_start: 0.7123 (t80) cc_final: 0.6835 (m-80) REVERT: C 441 MET cc_start: 0.8667 (mmm) cc_final: 0.8406 (mmm) REVERT: C 511 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7325 (ttmt) REVERT: C 643 MET cc_start: 0.8845 (mtt) cc_final: 0.8524 (mtt) REVERT: C 666 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8029 (mm-30) REVERT: C 853 ARG cc_start: 0.7248 (mpp80) cc_final: 0.6984 (mtm110) REVERT: C 874 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8303 (ttmt) outliers start: 16 outliers final: 10 residues processed: 309 average time/residue: 0.6634 time to fit residues: 234.1503 Evaluate side-chains 307 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 297 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 878 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain C residue 435 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: 0.7980 chunk 221 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106082 restraints weight = 40018.967| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.22 r_work: 0.2999 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23864 Z= 0.110 Angle : 0.515 14.130 32388 Z= 0.259 Chirality : 0.038 0.147 3676 Planarity : 0.004 0.044 3992 Dihedral : 8.973 88.780 3948 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 15.62 % Favored : 83.51 % 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: 1.56 (0.16), residues: 2908 helix: 1.96 (0.12), residues: 2048 sheet: None (None), residues: 0 loop : -1.31 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.013 0.001 TYR B 209 PHE 0.018 0.001 PHE A 548 TRP 0.017 0.001 TRP C 391 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00254 (23860) covalent geometry : angle 0.51541 (32380) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.11051 ( 8) hydrogen bonds : bond 0.03857 ( 1340) hydrogen bonds : angle 2.96658 ( 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 313 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 293 time to evaluate : 0.886 Fit side-chains REVERT: A 259 ASN cc_start: 0.7998 (m-40) cc_final: 0.7419 (p0) REVERT: A 407 PHE cc_start: 0.7142 (t80) cc_final: 0.6709 (m-80) REVERT: A 441 MET cc_start: 0.8785 (mmm) cc_final: 0.8524 (mmm) REVERT: A 643 MET cc_start: 0.8938 (mtt) cc_final: 0.8717 (mtt) REVERT: A 666 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8246 (mm-30) REVERT: A 874 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8440 (ttmt) REVERT: D 259 ASN cc_start: 0.7991 (m-40) cc_final: 0.7429 (p0) REVERT: D 407 PHE cc_start: 0.7044 (t80) cc_final: 0.6714 (m-80) REVERT: D 441 MET cc_start: 0.8812 (mmm) cc_final: 0.8534 (mmm) REVERT: D 584 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.7873 (mt) REVERT: D 643 MET cc_start: 0.8941 (mtt) cc_final: 0.8721 (mtt) REVERT: D 666 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8239 (mm-30) REVERT: D 853 ARG cc_start: 0.7443 (mpp80) cc_final: 0.7232 (mtm110) REVERT: D 874 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8439 (ttmt) REVERT: B 259 ASN cc_start: 0.8000 (m-40) cc_final: 0.7426 (p0) REVERT: B 407 PHE cc_start: 0.7147 (t80) cc_final: 0.6720 (m-80) REVERT: B 441 MET cc_start: 0.8784 (mmm) cc_final: 0.8523 (mmm) REVERT: B 584 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 643 MET cc_start: 0.8942 (mtt) cc_final: 0.8720 (mtt) REVERT: B 666 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 853 ARG cc_start: 0.7442 (mpp80) cc_final: 0.7229 (mtm110) REVERT: B 874 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8444 (ttmt) REVERT: C 259 ASN cc_start: 0.7943 (m-40) cc_final: 0.7411 (p0) REVERT: C 407 PHE cc_start: 0.7136 (t80) cc_final: 0.6711 (m-80) REVERT: C 441 MET cc_start: 0.8783 (mmm) cc_final: 0.8524 (mmm) REVERT: C 643 MET cc_start: 0.8939 (mtt) cc_final: 0.8719 (mtt) REVERT: C 666 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 874 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8442 (ttmt) outliers start: 20 outliers final: 7 residues processed: 304 average time/residue: 0.6623 time to fit residues: 229.9045 Evaluate side-chains 301 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 292 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 878 GLU 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 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: 2.9990 chunk 175 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108162 restraints weight = 44357.808| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.50 r_work: 0.2939 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2130 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= 0.115 Angle : 0.526 14.037 32388 Z= 0.262 Chirality : 0.038 0.147 3676 Planarity : 0.004 0.043 3992 Dihedral : 8.854 89.312 3948 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.48 % Allowed : 16.06 % Favored : 83.46 % 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: 1.62 (0.16), residues: 2908 helix: 2.00 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.28 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 437 TYR 0.015 0.001 TYR D 209 PHE 0.010 0.001 PHE D 419 TRP 0.020 0.001 TRP B 391 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00271 (23860) covalent geometry : angle 0.52581 (32380) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.14698 ( 8) hydrogen bonds : bond 0.03932 ( 1340) hydrogen bonds : angle 2.95730 ( 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 301 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 290 time to evaluate : 0.973 Fit side-chains REVERT: A 259 ASN cc_start: 0.7987 (m-40) cc_final: 0.7403 (p0) REVERT: A 407 PHE cc_start: 0.7121 (t80) cc_final: 0.6701 (m-80) REVERT: A 441 MET cc_start: 0.8784 (mmm) cc_final: 0.8518 (mmm) REVERT: A 511 LYS cc_start: 0.7275 (ttmm) cc_final: 0.7062 (ttmt) REVERT: A 643 MET cc_start: 0.8929 (mtt) cc_final: 0.8725 (mtt) REVERT: A 666 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 874 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8417 (ttmt) REVERT: D 259 ASN cc_start: 0.7974 (m-40) cc_final: 0.7402 (p0) REVERT: D 407 PHE cc_start: 0.7131 (t80) cc_final: 0.6705 (m-80) REVERT: D 441 MET cc_start: 0.8819 (mmm) cc_final: 0.8544 (mmm) REVERT: D 511 LYS cc_start: 0.7299 (ttmm) cc_final: 0.7085 (ttmt) REVERT: D 584 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8147 (mt) REVERT: D 643 MET cc_start: 0.8933 (mtt) cc_final: 0.8731 (mtt) REVERT: D 666 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 853 ARG cc_start: 0.7421 (mpp80) cc_final: 0.7217 (mtm110) REVERT: D 874 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8424 (ttmt) REVERT: B 259 ASN cc_start: 0.7984 (m-40) cc_final: 0.7407 (p0) REVERT: B 407 PHE cc_start: 0.7123 (t80) cc_final: 0.6703 (m-80) REVERT: B 441 MET cc_start: 0.8793 (mmm) cc_final: 0.8529 (mmm) REVERT: B 511 LYS cc_start: 0.7271 (ttmm) cc_final: 0.7055 (ttmt) REVERT: B 584 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8140 (mt) REVERT: B 643 MET cc_start: 0.8934 (mtt) cc_final: 0.8731 (mtt) REVERT: B 666 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8233 (mm-30) REVERT: B 853 ARG cc_start: 0.7405 (mpp80) cc_final: 0.7204 (mtm110) REVERT: B 874 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8423 (ttmt) REVERT: C 259 ASN cc_start: 0.7935 (m-40) cc_final: 0.7393 (p0) REVERT: C 407 PHE cc_start: 0.7117 (t80) cc_final: 0.6705 (m-80) REVERT: C 441 MET cc_start: 0.8773 (mmm) cc_final: 0.8455 (mmm) REVERT: C 511 LYS cc_start: 0.7282 (ttmm) cc_final: 0.7067 (ttmt) REVERT: C 643 MET cc_start: 0.8935 (mtt) cc_final: 0.8732 (mtt) REVERT: C 666 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 874 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8422 (ttmt) outliers start: 11 outliers final: 8 residues processed: 296 average time/residue: 0.6494 time to fit residues: 220.1779 Evaluate side-chains 300 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 290 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 878 GLU 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 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: 2.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 123 optimal weight: 0.6980 chunk 245 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104803 restraints weight = 35846.955| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.04 r_work: 0.2966 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 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 = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23864 Z= 0.138 Angle : 0.552 12.812 32388 Z= 0.276 Chirality : 0.039 0.148 3676 Planarity : 0.004 0.043 3992 Dihedral : 8.787 89.782 3948 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.52 % Allowed : 15.92 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2908 helix: 1.94 (0.12), residues: 2052 sheet: None (None), residues: 0 loop : -1.32 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 437 TYR 0.018 0.002 TYR C 209 PHE 0.020 0.001 PHE D 548 TRP 0.022 0.002 TRP A 391 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00335 (23860) covalent geometry : angle 0.55242 (32380) SS BOND : bond 0.00392 ( 4) SS BOND : angle 0.30219 ( 8) hydrogen bonds : bond 0.04365 ( 1340) hydrogen bonds : angle 3.02269 ( 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 310 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 298 time to evaluate : 0.831 Fit side-chains REVERT: A 259 ASN cc_start: 0.7989 (m-40) cc_final: 0.7421 (p0) REVERT: A 407 PHE cc_start: 0.7073 (t80) cc_final: 0.6724 (m-80) REVERT: A 441 MET cc_start: 0.8775 (mmm) cc_final: 0.8511 (mmm) REVERT: A 511 LYS cc_start: 0.7208 (ttmm) cc_final: 0.6988 (ttmt) REVERT: A 585 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7410 (mmmm) REVERT: A 643 MET cc_start: 0.8960 (mtt) cc_final: 0.8720 (mtt) REVERT: A 666 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8226 (mm-30) REVERT: A 874 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8424 (ttmt) REVERT: D 259 ASN cc_start: 0.7989 (m-40) cc_final: 0.7422 (p0) REVERT: D 407 PHE cc_start: 0.7074 (t80) cc_final: 0.6718 (m-80) REVERT: D 441 MET cc_start: 0.8810 (mmm) cc_final: 0.8529 (mmm) REVERT: D 511 LYS cc_start: 0.7235 (ttmm) cc_final: 0.7013 (ttmt) REVERT: D 584 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8267 (mt) REVERT: D 643 MET cc_start: 0.8966 (mtt) cc_final: 0.8728 (mtt) REVERT: D 666 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8238 (mm-30) REVERT: D 874 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8429 (ttmt) REVERT: B 259 ASN cc_start: 0.7985 (m-40) cc_final: 0.7417 (p0) REVERT: B 407 PHE cc_start: 0.7075 (t80) cc_final: 0.6731 (m-80) REVERT: B 511 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6994 (ttmt) REVERT: B 584 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 643 MET cc_start: 0.8957 (mtt) cc_final: 0.8715 (mtt) REVERT: B 666 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 853 ARG cc_start: 0.7390 (mpp80) cc_final: 0.7186 (mtm110) REVERT: B 874 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8427 (ttmt) REVERT: C 259 ASN cc_start: 0.7931 (m-40) cc_final: 0.7398 (p0) REVERT: C 407 PHE cc_start: 0.7061 (t80) cc_final: 0.6719 (m-80) REVERT: C 441 MET cc_start: 0.8783 (mmm) cc_final: 0.8517 (mmm) REVERT: C 511 LYS cc_start: 0.7221 (ttmm) cc_final: 0.6997 (ttmt) REVERT: C 585 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7459 (mmmm) REVERT: C 643 MET cc_start: 0.8966 (mtt) cc_final: 0.8727 (mtt) REVERT: C 666 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8235 (mm-30) REVERT: C 874 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8424 (ttmt) outliers start: 12 outliers final: 8 residues processed: 306 average time/residue: 0.6103 time to fit residues: 214.6636 Evaluate side-chains 305 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 295 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 878 GLU 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 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: 2.9990 chunk 87 optimal weight: 0.7980 chunk 262 optimal weight: 0.0970 chunk 206 optimal weight: 0.6980 chunk 116 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 291 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN C 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109936 restraints weight = 42242.514| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.29 r_work: 0.3038 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23864 Z= 0.097 Angle : 0.514 12.840 32388 Z= 0.254 Chirality : 0.037 0.148 3676 Planarity : 0.004 0.044 3992 Dihedral : 8.346 88.297 3948 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.57 % Allowed : 15.84 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.16), residues: 2908 helix: 2.20 (0.12), residues: 2060 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 437 TYR 0.012 0.001 TYR A 708 PHE 0.012 0.001 PHE D 419 TRP 0.014 0.001 TRP C 391 HIS 0.001 0.000 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00215 (23860) covalent geometry : angle 0.51395 (32380) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.06959 ( 8) hydrogen bonds : bond 0.03403 ( 1340) hydrogen bonds : angle 2.88895 ( 3980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8577.13 seconds wall clock time: 146 minutes 17.93 seconds (8777.93 seconds total)