Starting phenix.real_space_refine on Sat Sep 12 18:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2026/6gyn_0093.map" } resolution = 3.4 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= 0.011 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 132 5.16 5 C 11148 2.51 5 N 2684 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C Time building chain proxies: 5.48, per 1000 atoms: 0.32 Number of scatterers: 16932 At special positions: 0 Unit cell: (132.66, 132.66, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 16 15.00 O 2952 8.00 N 2684 7.00 C 11148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 429 " distance=0.00 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 434 " distance=0.00 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 449 " distance=0.00 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 478 " distance=0.00 Simple disulfide: pdb=" SG CYS C 505 " - pdb=" SG CYS C 505 " distance=0.00 Simple disulfide: pdb=" SG CYS C 586 " - pdb=" SG CYS C 586 " distance=0.00 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 662 " distance=0.00 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 679 " distance=0.00 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: 1.33 Conformation dependent library (CDL) restraints added in 764.2 milliseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 70.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 259 through 286 removed outlier: 3.759A pdb=" N PHE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 292 through 313 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP A 345 " --> pdb=" O TRP A 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.564A pdb=" N ARG A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 390 through 410 removed outlier: 3.792A pdb=" N ILE A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.527A pdb=" N GLN A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 488 through 518 removed outlier: 3.699A pdb=" N TRP A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 259 through 286 removed outlier: 3.758A pdb=" N PHE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Proline residue: B 281 - end of helix Processing helix chain 'B' and resid 292 through 313 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.893A pdb=" N LYS B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 350 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Proline residue: B 440 - end of helix removed outlier: 3.526A pdb=" N GLN B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 4.020A pdb=" N GLU B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 696 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 Processing helix chain 'C' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU C 222 " --> pdb=" O PHE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Proline residue: C 281 - end of helix Processing helix chain 'C' and resid 292 through 313 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP C 345 " --> pdb=" O TRP C 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Proline residue: C 440 - end of helix removed outlier: 3.525A pdb=" N GLN C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP C 493 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR C 559 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 573 Processing helix chain 'C' and resid 574 through 591 removed outlier: 5.580A pdb=" N LYS C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU C 589 " --> pdb=" O ASN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 Processing helix chain 'C' and resid 609 through 611 No H-bonds generated for 'chain 'C' and resid 609 through 611' Processing helix chain 'C' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 696 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 708 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Proline residue: D 281 - end of helix Processing helix chain 'D' and resid 292 through 313 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS D 339 " --> pdb=" O MET D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP D 345 " --> pdb=" O TRP D 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 350 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 410 " --> pdb=" O HIS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 443 removed outlier: 3.694A pdb=" N PHE D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Proline residue: D 440 - end of helix removed outlier: 3.525A pdb=" N GLN D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 460 through 475 Processing helix chain 'D' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP D 493 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR D 559 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 Processing helix chain 'D' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU D 589 " --> pdb=" O ASN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 609 through 611 No H-bonds generated for 'chain 'D' and resid 609 through 611' Processing helix chain 'D' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 696 " --> pdb=" O VAL D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 616 removed outlier: 6.574A pdb=" N ARG A 680 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR A 621 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 675 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 612 through 616 removed outlier: 6.572A pdb=" N ARG B 680 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR B 621 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 675 " --> pdb=" O TYR B 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG C 680 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR C 621 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 675 " --> pdb=" O TYR C 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG D 680 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR D 621 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 675 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2552 1.32 - 1.44: 4691 1.44 - 1.56: 9773 1.56 - 1.68: 32 1.68 - 1.80: 232 Bond restraints: 17280 Sorted by residual: bond pdb=" O13 3PE B 806 " pdb=" P 3PE B 806 " ideal model delta sigma weight residual 1.654 1.592 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O13 3PE D 808 " pdb=" P 3PE D 808 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O13 3PE C 806 " pdb=" P 3PE C 806 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O13 3PE A 804 " pdb=" P 3PE A 804 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O13 PC1 B 803 " pdb=" P PC1 B 803 " ideal model delta sigma weight residual 1.652 1.593 0.059 2.00e-02 2.50e+03 8.66e+00 ... (remaining 17275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 21576 1.50 - 3.00: 1278 3.00 - 4.51: 237 4.51 - 6.01: 41 6.01 - 7.51: 20 Bond angle restraints: 23152 Sorted by residual: angle pdb=" C GLY D 480 " pdb=" N TYR D 481 " pdb=" CA TYR D 481 " ideal model delta sigma weight residual 121.70 129.07 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C GLY C 480 " pdb=" N TYR C 481 " pdb=" CA TYR C 481 " ideal model delta sigma weight residual 121.70 129.05 -7.35 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C GLY A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta sigma weight residual 121.70 129.04 -7.34 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C GLY B 480 " pdb=" N TYR B 481 " pdb=" CA TYR B 481 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 angle pdb=" C ARG C 390 " pdb=" N LEU C 391 " pdb=" CA LEU C 391 " ideal model delta sigma weight residual 120.28 123.91 -3.63 1.44e+00 4.82e-01 6.34e+00 ... (remaining 23147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.05: 9366 11.05 - 22.10: 786 22.10 - 33.16: 128 33.16 - 44.21: 52 44.21 - 55.26: 28 Dihedral angle restraints: 10360 sinusoidal: 4532 harmonic: 5828 Sorted by residual: dihedral pdb=" CA GLY A 480 " pdb=" C GLY A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 0.00 -21.88 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLY B 480 " pdb=" C GLY B 480 " pdb=" N TYR B 481 " pdb=" CA TYR B 481 " ideal model delta harmonic sigma weight residual 0.00 -21.82 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLY D 480 " pdb=" C GLY D 480 " pdb=" N TYR D 481 " pdb=" CA TYR D 481 " ideal model delta harmonic sigma weight residual 0.00 -21.80 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 10357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2010 0.065 - 0.130: 458 0.130 - 0.195: 20 0.195 - 0.259: 0 0.259 - 0.324: 4 Chirality restraints: 2492 Sorted by residual: chirality pdb=" C2 PC1 C 801 " pdb=" C1 PC1 C 801 " pdb=" C3 PC1 C 801 " pdb=" O21 PC1 C 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2 PC1 B 801 " pdb=" C1 PC1 B 801 " pdb=" C3 PC1 B 801 " pdb=" O21 PC1 B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C2 PC1 A 808 " pdb=" C1 PC1 A 808 " pdb=" C3 PC1 A 808 " pdb=" O21 PC1 A 808 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2489 not shown) Planarity restraints: 2820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 439 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 440 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 439 " 0.035 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C 440 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 440 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 440 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 439 " 0.035 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO D 440 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 440 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 440 " 0.029 5.00e-02 4.00e+02 ... (remaining 2817 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4380 2.80 - 3.32: 15005 3.32 - 3.85: 27134 3.85 - 4.37: 31929 4.37 - 4.90: 55826 Nonbonded interactions: 134274 Sorted by model distance: nonbonded pdb=" OG SER C 641 " pdb=" OD2 ASP C 676 " model vdw 2.273 3.040 nonbonded pdb=" OG SER D 641 " pdb=" OD2 ASP D 676 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 641 " pdb=" OD2 ASP B 676 " model vdw 2.273 3.040 nonbonded pdb=" OG SER A 641 " pdb=" OD2 ASP A 676 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG C 378 " pdb=" O LEU C 442 " model vdw 2.344 3.120 ... (remaining 134269 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'B' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'C' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'D' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.300 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.062 17280 Z= 0.353 Angle : 0.849 7.511 23160 Z= 0.454 Chirality : 0.052 0.324 2492 Planarity : 0.006 0.052 2820 Dihedral : 9.321 55.262 6584 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 1972 helix: -1.78 (0.11), residues: 1312 sheet: 0.54 (0.48), residues: 116 loop : -1.46 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 396 TYR 0.032 0.003 TYR C 633 PHE 0.024 0.002 PHE B 379 TRP 0.022 0.003 TRP A 401 HIS 0.010 0.002 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.35 (17280) covalent geometry : angle 0.84944 / 0.45 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.14292 / 9.24 ( 1016) hydrogen bonds : angle 5.95152 / 4.32 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8756 (mmm) cc_final: 0.8070 (mpp) REVERT: A 331 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7480 (mm-40) REVERT: A 335 MET cc_start: 0.7963 (mmm) cc_final: 0.7503 (mmm) REVERT: A 407 MET cc_start: 0.8456 (tpp) cc_final: 0.8184 (tpt) REVERT: A 432 ASP cc_start: 0.8659 (t70) cc_final: 0.8379 (t70) REVERT: B 308 ILE cc_start: 0.8976 (mt) cc_final: 0.8773 (tt) REVERT: B 331 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 335 MET cc_start: 0.8080 (mmm) cc_final: 0.7592 (mmm) REVERT: B 407 MET cc_start: 0.8465 (tpp) cc_final: 0.8168 (tpt) REVERT: B 432 ASP cc_start: 0.8657 (t70) cc_final: 0.8359 (t70) REVERT: B 449 CYS cc_start: 0.8414 (p) cc_final: 0.8123 (p) REVERT: C 308 ILE cc_start: 0.8972 (mt) cc_final: 0.8771 (tt) REVERT: C 331 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7457 (mm-40) REVERT: C 335 MET cc_start: 0.8086 (mmm) cc_final: 0.7598 (mmm) REVERT: C 407 MET cc_start: 0.8464 (tpp) cc_final: 0.8167 (tpt) REVERT: C 432 ASP cc_start: 0.8655 (t70) cc_final: 0.8355 (t70) REVERT: C 449 CYS cc_start: 0.8407 (p) cc_final: 0.8121 (p) REVERT: D 308 ILE cc_start: 0.8974 (mt) cc_final: 0.8771 (tt) REVERT: D 331 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7455 (mm-40) REVERT: D 335 MET cc_start: 0.8087 (mmm) cc_final: 0.7599 (mmm) REVERT: D 407 MET cc_start: 0.8461 (tpp) cc_final: 0.8165 (tpt) REVERT: D 432 ASP cc_start: 0.8652 (t70) cc_final: 0.8356 (t70) REVERT: D 449 CYS cc_start: 0.8400 (p) cc_final: 0.8127 (p) REVERT: D 473 MET cc_start: 0.8525 (ttm) cc_final: 0.8233 (ttm) REVERT: D 593 MET cc_start: 0.8534 (ttt) cc_final: 0.8333 (ttt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1336 time to fit residues: 61.3013 Evaluate side-chains 162 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS A 459 ASN A 541 HIS A 602 ASN B 406 HIS B 459 ASN B 541 HIS C 406 HIS C 459 ASN C 541 HIS C 602 ASN D 406 HIS D 459 ASN D 541 HIS D 602 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085997 restraints weight = 30338.325| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.45 r_work: 0.2988 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17280 Z= 0.110 Angle : 0.510 6.805 23160 Z= 0.262 Chirality : 0.040 0.130 2492 Planarity : 0.004 0.034 2820 Dihedral : 7.802 54.401 2784 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.76 % Allowed : 8.78 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.13 (0.18), residues: 1972 helix: 0.50 (0.13), residues: 1340 sheet: 0.77 (0.48), residues: 116 loop : -0.93 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 550 TYR 0.013 0.001 TYR C 531 PHE 0.011 0.001 PHE C 689 TRP 0.017 0.001 TRP A 401 HIS 0.003 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (17280) covalent geometry : angle 0.51013 / 0.26 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03700 / 2.44 ( 1016) hydrogen bonds : angle 4.11240 / 2.98 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.551 Fit side-chains REVERT: A 214 MET cc_start: 0.6604 (mtt) cc_final: 0.6290 (mmm) REVERT: A 269 MET cc_start: 0.8589 (mmm) cc_final: 0.8078 (tpp) REVERT: A 304 THR cc_start: 0.9508 (m) cc_final: 0.9287 (p) REVERT: A 331 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7454 (mm-40) REVERT: A 335 MET cc_start: 0.8331 (mmm) cc_final: 0.7874 (mmm) REVERT: B 214 MET cc_start: 0.6618 (mtt) cc_final: 0.6274 (mmm) REVERT: B 304 THR cc_start: 0.9412 (m) cc_final: 0.9198 (p) REVERT: B 331 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7470 (mm-40) REVERT: B 335 MET cc_start: 0.8336 (mmm) cc_final: 0.7882 (mmm) REVERT: B 449 CYS cc_start: 0.8182 (p) cc_final: 0.7740 (p) REVERT: C 214 MET cc_start: 0.6639 (mtt) cc_final: 0.6279 (mmm) REVERT: C 304 THR cc_start: 0.9411 (m) cc_final: 0.9198 (p) REVERT: C 331 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7462 (mm-40) REVERT: C 335 MET cc_start: 0.8325 (mmm) cc_final: 0.7873 (mmm) REVERT: C 449 CYS cc_start: 0.8211 (p) cc_final: 0.7770 (p) REVERT: D 214 MET cc_start: 0.6609 (mtt) cc_final: 0.6282 (mmm) REVERT: D 304 THR cc_start: 0.9411 (m) cc_final: 0.9199 (p) REVERT: D 331 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7463 (mm-40) REVERT: D 335 MET cc_start: 0.8338 (mmm) cc_final: 0.7887 (mmm) REVERT: D 449 CYS cc_start: 0.8210 (p) cc_final: 0.7769 (p) REVERT: D 473 MET cc_start: 0.8891 (ttm) cc_final: 0.8623 (ttm) outliers start: 13 outliers final: 4 residues processed: 228 average time/residue: 0.1151 time to fit residues: 42.5847 Evaluate side-chains 175 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 187 optimal weight: 0.0670 chunk 53 optimal weight: 0.3980 chunk 167 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 HIS B 475 HIS C 475 HIS D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086639 restraints weight = 30844.141| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.46 r_work: 0.3002 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17280 Z= 0.089 Angle : 0.466 5.472 23160 Z= 0.238 Chirality : 0.039 0.127 2492 Planarity : 0.003 0.033 2820 Dihedral : 7.554 54.166 2784 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 10.29 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.33 (0.19), residues: 1972 helix: 1.50 (0.14), residues: 1296 sheet: 0.97 (0.49), residues: 116 loop : -0.51 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 674 TYR 0.013 0.001 TYR B 531 PHE 0.014 0.001 PHE A 252 TRP 0.017 0.001 TRP A 401 HIS 0.001 0.001 HIS C 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (17280) covalent geometry : angle 0.46587 / 0.24 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03193 / 2.12 ( 1016) hydrogen bonds : angle 3.80038 / 2.75 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.521 Fit side-chains REVERT: A 331 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 335 MET cc_start: 0.8197 (mmm) cc_final: 0.7765 (mmm) REVERT: A 449 CYS cc_start: 0.8278 (p) cc_final: 0.7730 (p) REVERT: A 538 MET cc_start: 0.8885 (mtm) cc_final: 0.8219 (mtm) REVERT: A 593 MET cc_start: 0.8193 (ttp) cc_final: 0.7899 (ttp) REVERT: B 304 THR cc_start: 0.9486 (m) cc_final: 0.9244 (p) REVERT: B 331 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7487 (mm-40) REVERT: B 335 MET cc_start: 0.8304 (mmm) cc_final: 0.7846 (mmm) REVERT: B 449 CYS cc_start: 0.8300 (p) cc_final: 0.7782 (p) REVERT: B 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8612 (mt) REVERT: B 593 MET cc_start: 0.8222 (ttp) cc_final: 0.7851 (ttp) REVERT: C 304 THR cc_start: 0.9485 (m) cc_final: 0.9245 (p) REVERT: C 331 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7483 (mm-40) REVERT: C 335 MET cc_start: 0.8303 (mmm) cc_final: 0.7848 (mmm) REVERT: C 449 CYS cc_start: 0.8294 (p) cc_final: 0.7776 (p) REVERT: C 494 LEU cc_start: 0.8899 (mt) cc_final: 0.8607 (mt) REVERT: C 593 MET cc_start: 0.8210 (ttp) cc_final: 0.7842 (ttp) REVERT: D 304 THR cc_start: 0.9484 (m) cc_final: 0.9246 (p) REVERT: D 331 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7439 (mm-40) REVERT: D 335 MET cc_start: 0.8309 (mmm) cc_final: 0.7856 (mmm) REVERT: D 449 CYS cc_start: 0.8331 (p) cc_final: 0.7815 (p) REVERT: D 473 MET cc_start: 0.8873 (ttm) cc_final: 0.8631 (ttm) REVERT: D 494 LEU cc_start: 0.8886 (mt) cc_final: 0.8600 (mt) REVERT: D 593 MET cc_start: 0.8192 (ttp) cc_final: 0.7807 (ttp) outliers start: 8 outliers final: 4 residues processed: 212 average time/residue: 0.0990 time to fit residues: 35.7928 Evaluate side-chains 184 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN D 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087181 restraints weight = 30476.512| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.42 r_work: 0.3008 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17280 Z= 0.092 Angle : 0.469 7.936 23160 Z= 0.234 Chirality : 0.039 0.128 2492 Planarity : 0.003 0.030 2820 Dihedral : 7.426 54.655 2784 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.64 % Allowed : 10.17 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.93 (0.19), residues: 1972 helix: 1.97 (0.14), residues: 1296 sheet: 0.91 (0.49), residues: 116 loop : -0.24 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 390 TYR 0.013 0.001 TYR A 531 PHE 0.006 0.001 PHE D 596 TRP 0.016 0.001 TRP A 401 HIS 0.001 0.000 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (17280) covalent geometry : angle 0.46901 / 0.23 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03045 / 2.01 ( 1016) hydrogen bonds : angle 3.62700 / 2.61 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.663 Fit side-chains REVERT: A 331 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7306 (mm-40) REVERT: A 335 MET cc_start: 0.8328 (mmm) cc_final: 0.7865 (mmm) REVERT: A 449 CYS cc_start: 0.8166 (p) cc_final: 0.7601 (p) REVERT: A 538 MET cc_start: 0.8912 (mtm) cc_final: 0.8495 (mtm) REVERT: A 593 MET cc_start: 0.8337 (ttp) cc_final: 0.8123 (ttp) REVERT: B 304 THR cc_start: 0.9476 (m) cc_final: 0.9244 (p) REVERT: B 331 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7412 (mm-40) REVERT: B 335 MET cc_start: 0.8267 (mmm) cc_final: 0.7816 (mmm) REVERT: B 449 CYS cc_start: 0.8176 (p) cc_final: 0.7611 (p) REVERT: B 538 MET cc_start: 0.8848 (mtm) cc_final: 0.8324 (mtm) REVERT: B 593 MET cc_start: 0.8359 (ttp) cc_final: 0.8118 (ttp) REVERT: C 304 THR cc_start: 0.9477 (m) cc_final: 0.9246 (p) REVERT: C 331 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7412 (mm-40) REVERT: C 335 MET cc_start: 0.8299 (mmm) cc_final: 0.7833 (mmm) REVERT: C 449 CYS cc_start: 0.8160 (p) cc_final: 0.7598 (p) REVERT: C 538 MET cc_start: 0.8840 (mtm) cc_final: 0.8127 (mtm) REVERT: C 593 MET cc_start: 0.8359 (ttp) cc_final: 0.8078 (ttp) REVERT: D 304 THR cc_start: 0.9475 (m) cc_final: 0.9245 (p) REVERT: D 331 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7366 (mm-40) REVERT: D 335 MET cc_start: 0.8335 (mmm) cc_final: 0.7874 (mmm) REVERT: D 449 CYS cc_start: 0.8172 (p) cc_final: 0.7604 (p) REVERT: D 473 MET cc_start: 0.8829 (ttm) cc_final: 0.8576 (ttm) REVERT: D 538 MET cc_start: 0.8839 (mtm) cc_final: 0.8126 (mtm) REVERT: D 593 MET cc_start: 0.8335 (ttp) cc_final: 0.8070 (ttp) outliers start: 11 outliers final: 8 residues processed: 203 average time/residue: 0.1108 time to fit residues: 37.5215 Evaluate side-chains 179 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 164 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN A 475 HIS B 475 HIS C 223 GLN C 475 HIS D 223 GLN D 475 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082188 restraints weight = 31084.102| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.45 r_work: 0.2926 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17280 Z= 0.202 Angle : 0.547 7.180 23160 Z= 0.278 Chirality : 0.043 0.133 2492 Planarity : 0.003 0.028 2820 Dihedral : 8.126 58.937 2784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.69 % Allowed : 9.19 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1972 helix: 2.14 (0.14), residues: 1300 sheet: 0.75 (0.48), residues: 116 loop : 0.04 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 372 TYR 0.018 0.002 TYR C 531 PHE 0.010 0.001 PHE B 584 TRP 0.017 0.002 TRP A 401 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (17280) covalent geometry : angle 0.54741 / 0.28 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03644 / 2.39 ( 1016) hydrogen bonds : angle 3.73587 / 2.67 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.679 Fit side-chains REVERT: A 303 ASP cc_start: 0.8480 (m-30) cc_final: 0.8079 (t0) REVERT: A 331 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7144 (mm-40) REVERT: A 335 MET cc_start: 0.8471 (mmm) cc_final: 0.7776 (mmm) REVERT: A 449 CYS cc_start: 0.8404 (p) cc_final: 0.7895 (p) REVERT: B 303 ASP cc_start: 0.8466 (m-30) cc_final: 0.8061 (t0) REVERT: B 304 THR cc_start: 0.9474 (m) cc_final: 0.9270 (p) REVERT: B 331 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7139 (mm-40) REVERT: B 335 MET cc_start: 0.8475 (mmm) cc_final: 0.7781 (mmm) REVERT: B 538 MET cc_start: 0.9003 (mtm) cc_final: 0.8646 (mtm) REVERT: C 303 ASP cc_start: 0.8459 (m-30) cc_final: 0.8055 (t0) REVERT: C 304 THR cc_start: 0.9474 (m) cc_final: 0.9269 (p) REVERT: C 331 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7167 (mm-40) REVERT: C 335 MET cc_start: 0.8463 (mmm) cc_final: 0.7767 (mmm) REVERT: C 538 MET cc_start: 0.8955 (mtm) cc_final: 0.8571 (mtp) REVERT: D 303 ASP cc_start: 0.8457 (m-30) cc_final: 0.8048 (t0) REVERT: D 304 THR cc_start: 0.9467 (m) cc_final: 0.9259 (p) REVERT: D 331 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7144 (mm-40) REVERT: D 335 MET cc_start: 0.8476 (mmm) cc_final: 0.7784 (mmm) REVERT: D 473 MET cc_start: 0.8995 (ttm) cc_final: 0.8767 (ttm) REVERT: D 538 MET cc_start: 0.8946 (mtm) cc_final: 0.8564 (mtp) outliers start: 29 outliers final: 10 residues processed: 179 average time/residue: 0.1034 time to fit residues: 31.4504 Evaluate side-chains 163 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 126 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 459 ASN B 475 HIS C 223 GLN C 459 ASN D 223 GLN D 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084063 restraints weight = 30878.768| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.44 r_work: 0.2954 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17280 Z= 0.123 Angle : 0.487 8.393 23160 Z= 0.246 Chirality : 0.040 0.131 2492 Planarity : 0.003 0.029 2820 Dihedral : 7.984 58.503 2784 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.93 % Allowed : 10.12 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.20), residues: 1972 helix: 2.28 (0.14), residues: 1304 sheet: 0.77 (0.48), residues: 116 loop : 0.10 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 390 TYR 0.016 0.001 TYR B 531 PHE 0.010 0.001 PHE C 658 TRP 0.016 0.001 TRP A 401 HIS 0.002 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17280) covalent geometry : angle 0.48696 / 0.25 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03246 / 2.15 ( 1016) hydrogen bonds : angle 3.58371 / 2.57 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.656 Fit side-chains REVERT: A 331 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7074 (mm-40) REVERT: A 335 MET cc_start: 0.8492 (mmm) cc_final: 0.7793 (mmm) REVERT: A 449 CYS cc_start: 0.8237 (p) cc_final: 0.7656 (p) REVERT: A 538 MET cc_start: 0.8879 (mtm) cc_final: 0.8182 (mtm) REVERT: A 593 MET cc_start: 0.8697 (ttp) cc_final: 0.7317 (ttp) REVERT: B 304 THR cc_start: 0.9473 (m) cc_final: 0.9264 (p) REVERT: B 331 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7066 (mm-40) REVERT: B 335 MET cc_start: 0.8429 (mmm) cc_final: 0.7742 (mmm) REVERT: B 538 MET cc_start: 0.8910 (mtm) cc_final: 0.8496 (mtm) REVERT: B 593 MET cc_start: 0.8693 (ttp) cc_final: 0.7329 (ttp) REVERT: C 304 THR cc_start: 0.9474 (m) cc_final: 0.9264 (p) REVERT: C 331 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7070 (mm-40) REVERT: C 335 MET cc_start: 0.8474 (mmm) cc_final: 0.7769 (mmm) REVERT: C 538 MET cc_start: 0.8915 (mtm) cc_final: 0.8437 (mtm) REVERT: C 593 MET cc_start: 0.8698 (ttp) cc_final: 0.7335 (ttp) REVERT: D 304 THR cc_start: 0.9477 (m) cc_final: 0.9269 (p) REVERT: D 331 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7070 (mm-40) REVERT: D 335 MET cc_start: 0.8474 (mmm) cc_final: 0.7765 (mmm) REVERT: D 473 MET cc_start: 0.8969 (ttm) cc_final: 0.8724 (ttm) REVERT: D 538 MET cc_start: 0.8907 (mtm) cc_final: 0.8426 (mtm) REVERT: D 593 MET cc_start: 0.8720 (ttp) cc_final: 0.7372 (ttp) outliers start: 16 outliers final: 14 residues processed: 174 average time/residue: 0.1126 time to fit residues: 32.5838 Evaluate side-chains 171 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 177 optimal weight: 0.0370 chunk 167 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 HIS C 223 GLN C 475 HIS D 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.084354 restraints weight = 30716.892| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.43 r_work: 0.2963 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17280 Z= 0.113 Angle : 0.481 8.517 23160 Z= 0.240 Chirality : 0.040 0.129 2492 Planarity : 0.003 0.029 2820 Dihedral : 7.742 55.693 2784 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 10.23 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.20), residues: 1972 helix: 2.42 (0.14), residues: 1304 sheet: 0.89 (0.48), residues: 116 loop : 0.16 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 390 TYR 0.016 0.001 TYR D 531 PHE 0.009 0.001 PHE B 658 TRP 0.016 0.001 TRP A 401 HIS 0.002 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (17280) covalent geometry : angle 0.48099 / 0.24 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03120 / 2.07 ( 1016) hydrogen bonds : angle 3.51335 / 2.52 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.654 Fit side-chains REVERT: A 303 ASP cc_start: 0.8449 (m-30) cc_final: 0.8137 (t0) REVERT: A 331 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7280 (mm-40) REVERT: A 335 MET cc_start: 0.8455 (mmm) cc_final: 0.7988 (mmm) REVERT: A 424 MET cc_start: 0.9251 (tpp) cc_final: 0.8481 (tpp) REVERT: A 449 CYS cc_start: 0.8130 (p) cc_final: 0.7551 (p) REVERT: A 538 MET cc_start: 0.8906 (mtm) cc_final: 0.8409 (mtm) REVERT: A 593 MET cc_start: 0.8660 (ttp) cc_final: 0.7375 (ttp) REVERT: B 331 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7279 (mm-40) REVERT: B 335 MET cc_start: 0.8462 (mmm) cc_final: 0.7995 (mmm) REVERT: B 424 MET cc_start: 0.9232 (tpp) cc_final: 0.8463 (tpp) REVERT: B 538 MET cc_start: 0.8990 (mtm) cc_final: 0.8676 (mtm) REVERT: B 593 MET cc_start: 0.8664 (ttp) cc_final: 0.7394 (ttp) REVERT: C 331 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7274 (mm-40) REVERT: C 335 MET cc_start: 0.8453 (mmm) cc_final: 0.7988 (mmm) REVERT: C 424 MET cc_start: 0.9241 (tpp) cc_final: 0.8473 (tpp) REVERT: C 538 MET cc_start: 0.8937 (mtm) cc_final: 0.8484 (mtm) REVERT: C 593 MET cc_start: 0.8666 (ttp) cc_final: 0.7396 (ttp) REVERT: D 304 THR cc_start: 0.9463 (m) cc_final: 0.9246 (p) REVERT: D 331 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7280 (mm-40) REVERT: D 335 MET cc_start: 0.8461 (mmm) cc_final: 0.7992 (mmm) REVERT: D 424 MET cc_start: 0.9240 (tpp) cc_final: 0.8910 (tpp) REVERT: D 473 MET cc_start: 0.8963 (ttm) cc_final: 0.8717 (ttm) REVERT: D 538 MET cc_start: 0.8940 (mtm) cc_final: 0.8479 (mtm) REVERT: D 593 MET cc_start: 0.8689 (ttp) cc_final: 0.7475 (ttp) outliers start: 23 outliers final: 7 residues processed: 174 average time/residue: 0.1135 time to fit residues: 33.1391 Evaluate side-chains 169 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 GLN C 223 GLN D 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084865 restraints weight = 30909.245| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.50 r_work: 0.2957 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17280 Z= 0.110 Angle : 0.473 7.363 23160 Z= 0.237 Chirality : 0.040 0.129 2492 Planarity : 0.003 0.029 2820 Dihedral : 7.454 50.699 2784 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.34 % Allowed : 10.41 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.20), residues: 1972 helix: 2.49 (0.14), residues: 1308 sheet: 1.00 (0.48), residues: 116 loop : 0.14 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 387 TYR 0.016 0.001 TYR D 531 PHE 0.007 0.001 PHE A 658 TRP 0.016 0.001 TRP C 401 HIS 0.002 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (17280) covalent geometry : angle 0.47278 / 0.24 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03066 / 2.04 ( 1016) hydrogen bonds : angle 3.46807 / 2.49 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.617 Fit side-chains REVERT: A 331 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7268 (mm-40) REVERT: A 335 MET cc_start: 0.8362 (mmm) cc_final: 0.7919 (mmm) REVERT: A 424 MET cc_start: 0.9236 (tpp) cc_final: 0.8438 (tpp) REVERT: A 449 CYS cc_start: 0.8135 (p) cc_final: 0.7549 (p) REVERT: A 538 MET cc_start: 0.8900 (mtm) cc_final: 0.8371 (mtm) REVERT: A 593 MET cc_start: 0.8654 (ttp) cc_final: 0.7350 (ttp) REVERT: B 331 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7266 (mm-40) REVERT: B 335 MET cc_start: 0.8354 (mmm) cc_final: 0.7909 (mmm) REVERT: B 424 MET cc_start: 0.9226 (tpp) cc_final: 0.8418 (tpp) REVERT: B 432 ASP cc_start: 0.8843 (t0) cc_final: 0.8622 (t0) REVERT: B 538 MET cc_start: 0.8981 (mtm) cc_final: 0.8743 (mtm) REVERT: B 593 MET cc_start: 0.8649 (ttp) cc_final: 0.7345 (ttp) REVERT: C 331 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7269 (mm-40) REVERT: C 335 MET cc_start: 0.8352 (mmm) cc_final: 0.7910 (mmm) REVERT: C 424 MET cc_start: 0.9231 (tpp) cc_final: 0.8905 (tpp) REVERT: C 432 ASP cc_start: 0.8839 (t0) cc_final: 0.8619 (t0) REVERT: C 538 MET cc_start: 0.8977 (mtm) cc_final: 0.8668 (mtm) REVERT: C 593 MET cc_start: 0.8647 (ttp) cc_final: 0.7351 (ttp) REVERT: D 303 ASP cc_start: 0.8441 (m-30) cc_final: 0.8069 (t0) REVERT: D 331 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7271 (mm-40) REVERT: D 335 MET cc_start: 0.8365 (mmm) cc_final: 0.7920 (mmm) REVERT: D 424 MET cc_start: 0.9238 (tpp) cc_final: 0.8908 (tpp) REVERT: D 473 MET cc_start: 0.8946 (ttm) cc_final: 0.8710 (ttm) REVERT: D 538 MET cc_start: 0.8980 (mtm) cc_final: 0.8669 (mtm) REVERT: D 593 MET cc_start: 0.8672 (ttp) cc_final: 0.7417 (ttp) outliers start: 23 outliers final: 12 residues processed: 180 average time/residue: 0.1087 time to fit residues: 32.9674 Evaluate side-chains 171 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 GLN C 223 GLN D 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085445 restraints weight = 30692.552| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.43 r_work: 0.2983 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17280 Z= 0.093 Angle : 0.509 10.945 23160 Z= 0.243 Chirality : 0.039 0.127 2492 Planarity : 0.003 0.029 2820 Dihedral : 7.161 55.771 2784 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.10 % Allowed : 10.87 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.20), residues: 1972 helix: 2.62 (0.14), residues: 1304 sheet: 1.15 (0.49), residues: 116 loop : 0.17 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 378 TYR 0.015 0.001 TYR A 531 PHE 0.008 0.001 PHE A 658 TRP 0.015 0.001 TRP A 401 HIS 0.002 0.000 HIS B 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (17280) covalent geometry : angle 0.50876 / 0.24 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.02934 / 1.95 ( 1016) hydrogen bonds : angle 3.42405 / 2.46 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.688 Fit side-chains REVERT: A 335 MET cc_start: 0.8250 (mmm) cc_final: 0.7611 (mmm) REVERT: A 424 MET cc_start: 0.9249 (tpp) cc_final: 0.8403 (tpp) REVERT: A 449 CYS cc_start: 0.8147 (p) cc_final: 0.7627 (p) REVERT: A 538 MET cc_start: 0.8937 (mtm) cc_final: 0.8562 (mtm) REVERT: A 593 MET cc_start: 0.8629 (ttp) cc_final: 0.7369 (ttp) REVERT: B 269 MET cc_start: 0.9057 (tpp) cc_final: 0.8855 (tpp) REVERT: B 331 GLN cc_start: 0.7603 (mm-40) cc_final: 0.6994 (mm-40) REVERT: B 335 MET cc_start: 0.8291 (mmm) cc_final: 0.7628 (mmm) REVERT: B 424 MET cc_start: 0.9234 (tpp) cc_final: 0.8376 (tpp) REVERT: B 432 ASP cc_start: 0.8865 (t0) cc_final: 0.8639 (t0) REVERT: B 538 MET cc_start: 0.8934 (mtm) cc_final: 0.8724 (mtm) REVERT: B 593 MET cc_start: 0.8626 (ttp) cc_final: 0.7331 (ttp) REVERT: C 269 MET cc_start: 0.9055 (tpp) cc_final: 0.8850 (tpp) REVERT: C 335 MET cc_start: 0.8286 (mmm) cc_final: 0.7618 (mmm) REVERT: C 424 MET cc_start: 0.9240 (tpp) cc_final: 0.8871 (tpp) REVERT: C 432 ASP cc_start: 0.8866 (t0) cc_final: 0.8639 (t0) REVERT: C 538 MET cc_start: 0.8968 (mtm) cc_final: 0.8730 (mtm) REVERT: C 593 MET cc_start: 0.8625 (ttp) cc_final: 0.7332 (ttp) REVERT: D 269 MET cc_start: 0.9058 (tpp) cc_final: 0.8854 (tpp) REVERT: D 303 ASP cc_start: 0.8414 (m-30) cc_final: 0.7926 (t0) REVERT: D 335 MET cc_start: 0.8304 (mmm) cc_final: 0.7635 (mmm) REVERT: D 424 MET cc_start: 0.9233 (tpp) cc_final: 0.8871 (tpp) REVERT: D 473 MET cc_start: 0.8942 (ttm) cc_final: 0.8705 (ttm) REVERT: D 538 MET cc_start: 0.8966 (mtm) cc_final: 0.8724 (mtm) REVERT: D 563 MET cc_start: 0.8939 (tpp) cc_final: 0.8686 (tpt) REVERT: D 593 MET cc_start: 0.8615 (ttp) cc_final: 0.7319 (ttp) outliers start: 19 outliers final: 9 residues processed: 193 average time/residue: 0.1217 time to fit residues: 38.0943 Evaluate side-chains 171 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 137 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 HIS C 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082989 restraints weight = 30946.509| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.45 r_work: 0.2944 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17280 Z= 0.144 Angle : 0.547 11.206 23160 Z= 0.266 Chirality : 0.041 0.153 2492 Planarity : 0.003 0.054 2820 Dihedral : 7.343 48.217 2784 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.87 % Allowed : 11.80 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.20), residues: 1972 helix: 2.59 (0.14), residues: 1308 sheet: 1.10 (0.48), residues: 116 loop : 0.20 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 378 TYR 0.017 0.001 TYR A 531 PHE 0.007 0.001 PHE B 658 TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (17280) covalent geometry : angle 0.54709 / 0.27 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.03242 / 2.14 ( 1016) hydrogen bonds : angle 3.52091 / 2.52 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.682 Fit side-chains REVERT: A 335 MET cc_start: 0.8190 (mmm) cc_final: 0.7559 (mmm) REVERT: A 424 MET cc_start: 0.9250 (tpp) cc_final: 0.8937 (tpp) REVERT: A 449 CYS cc_start: 0.8237 (p) cc_final: 0.7650 (p) REVERT: A 538 MET cc_start: 0.8994 (mtm) cc_final: 0.8639 (mtp) REVERT: A 593 MET cc_start: 0.8677 (ttp) cc_final: 0.7437 (ttp) REVERT: B 335 MET cc_start: 0.8223 (mmm) cc_final: 0.7577 (mmm) REVERT: B 424 MET cc_start: 0.9232 (tpp) cc_final: 0.8910 (tpp) REVERT: B 538 MET cc_start: 0.8983 (mtm) cc_final: 0.8779 (mtm) REVERT: B 593 MET cc_start: 0.8645 (ttp) cc_final: 0.7325 (ttp) REVERT: C 335 MET cc_start: 0.8224 (mmm) cc_final: 0.7576 (mmm) REVERT: C 424 MET cc_start: 0.9239 (tpp) cc_final: 0.8916 (tpp) REVERT: C 538 MET cc_start: 0.9010 (mtm) cc_final: 0.8756 (mtm) REVERT: C 593 MET cc_start: 0.8649 (ttp) cc_final: 0.7338 (ttp) REVERT: D 335 MET cc_start: 0.8246 (mmm) cc_final: 0.7583 (mmm) REVERT: D 424 MET cc_start: 0.9262 (tpp) cc_final: 0.8914 (tpp) REVERT: D 473 MET cc_start: 0.8952 (ttm) cc_final: 0.8748 (ttm) REVERT: D 538 MET cc_start: 0.9014 (mtm) cc_final: 0.8736 (mtm) REVERT: D 593 MET cc_start: 0.8661 (ttp) cc_final: 0.7394 (ttp) outliers start: 15 outliers final: 11 residues processed: 161 average time/residue: 0.1081 time to fit residues: 29.5617 Evaluate side-chains 161 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 158 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 178 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085117 restraints weight = 30549.847| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.47 r_work: 0.2978 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17280 Z= 0.097 Angle : 0.517 11.041 23160 Z= 0.250 Chirality : 0.039 0.132 2492 Planarity : 0.003 0.061 2820 Dihedral : 7.147 55.203 2784 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.76 % Allowed : 11.98 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.20), residues: 1972 helix: 2.68 (0.14), residues: 1304 sheet: 1.20 (0.48), residues: 116 loop : 0.22 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 578 TYR 0.015 0.001 TYR A 531 PHE 0.007 0.001 PHE D 658 TRP 0.015 0.001 TRP A 401 HIS 0.002 0.000 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (17280) covalent geometry : angle 0.51748 / 0.25 (23152) SS BOND : angle 0.00000 / 0.00 ( 8) hydrogen bonds : bond 0.02945 / 1.95 ( 1016) hydrogen bonds : angle 3.45464 / 2.47 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.71 seconds wall clock time: 57 minutes 17.67 seconds (3437.67 seconds total)