Starting phenix.real_space_refine on Sun Jun 15 17:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_0093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_0093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_0093.map" model { file = "/net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_0093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyn_0093/06_2025/6gyn_0093.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: 242 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: "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: 242 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: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C Time building chain proxies: 12.99, per 1000 atoms: 0.77 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.79 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: 5.18 Time building geometry restraints manager: 4.88 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 - 14.30: 9886 14.30 - 28.61: 458 28.61 - 42.91: 116 42.91 - 57.21: 60 57.21 - 71.51: 16 Dihedral angle restraints: 10536 sinusoidal: 4708 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 10533 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: 0.04 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: 0.680 Set stop_for_unknowns flag: 0.010 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.140 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 10.497 71.515 6760 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP A 401 HIS 0.010 0.002 HIS D 475 PHE 0.024 0.002 PHE B 379 TYR 0.032 0.003 TYR C 633 ARG 0.009 0.001 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.14292 ( 1016) hydrogen bonds : angle 5.95152 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00801 (17280) covalent geometry : angle 0.84944 (23152) *********************** 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 : 1.950 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: 0.7481 (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: 0.8380 (t70) REVERT: B 308 ILE cc_start: 0.8976 (mt) cc_final: 0.8775 (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: 0.7591 (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: 0.8363 (t70) REVERT: B 449 CYS cc_start: 0.8414 (p) cc_final: 0.8126 (p) REVERT: C 308 ILE cc_start: 0.8972 (mt) cc_final: 0.8770 (tt) REVERT: C 331 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7455 (mm-40) REVERT: C 335 MET cc_start: 0.8086 (mmm) cc_final: 0.7599 (mmm) REVERT: C 407 MET cc_start: 0.8464 (tpp) cc_final: 0.8166 (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: 0.8113 (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: 0.7454 (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: 0.8355 (t70) REVERT: D 449 CYS cc_start: 0.8400 (p) cc_final: 0.8128 (p) REVERT: D 473 MET cc_start: 0.8524 (ttm) cc_final: 0.8233 (ttm) REVERT: D 593 MET cc_start: 0.8534 (ttt) cc_final: 0.8334 (ttt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2907 time to fit residues: 132.3829 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 : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 541 HIS B 459 ASN B 541 HIS C 223 GLN C 459 ASN C 541 HIS D 223 GLN D 459 ASN D 541 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082596 restraints weight = 30588.795| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.44 r_work: 0.2930 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17280 Z= 0.191 Angle : 0.573 7.772 23160 Z= 0.294 Chirality : 0.043 0.123 2492 Planarity : 0.004 0.033 2820 Dihedral : 10.401 72.477 2960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 1972 helix: 0.45 (0.13), residues: 1340 sheet: 0.67 (0.48), residues: 116 loop : -0.89 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 401 HIS 0.005 0.002 HIS A 475 PHE 0.012 0.001 PHE B 689 TYR 0.016 0.002 TYR B 633 ARG 0.002 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1016) hydrogen bonds : angle 4.14727 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00439 (17280) covalent geometry : angle 0.57290 (23152) *********************** 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 218 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 2.266 Fit side-chains REVERT: A 304 THR cc_start: 0.9526 (m) cc_final: 0.9294 (p) REVERT: A 331 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7246 (mm-40) REVERT: A 335 MET cc_start: 0.8408 (mmm) cc_final: 0.7755 (mmm) REVERT: B 304 THR cc_start: 0.9431 (m) cc_final: 0.9207 (p) REVERT: B 331 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7244 (mm-40) REVERT: B 335 MET cc_start: 0.8396 (mmm) cc_final: 0.7700 (mmm) REVERT: C 304 THR cc_start: 0.9432 (m) cc_final: 0.9208 (p) REVERT: C 331 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7233 (mm-40) REVERT: C 335 MET cc_start: 0.8359 (mmm) cc_final: 0.7702 (mmm) REVERT: D 304 THR cc_start: 0.9430 (m) cc_final: 0.9207 (p) REVERT: D 331 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7233 (mm-40) REVERT: D 335 MET cc_start: 0.8369 (mmm) cc_final: 0.7714 (mmm) REVERT: D 473 MET cc_start: 0.8961 (ttm) cc_final: 0.8707 (ttm) outliers start: 20 outliers final: 9 residues processed: 210 average time/residue: 0.2995 time to fit residues: 100.7123 Evaluate side-chains 172 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 398 ILE 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 182 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS C 223 GLN C 475 HIS D 223 GLN D 475 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085696 restraints weight = 30537.457| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.46 r_work: 0.2982 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1971 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= 0.097 Angle : 0.477 6.077 23160 Z= 0.244 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.033 2820 Dihedral : 9.813 66.311 2960 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.87 % Allowed : 9.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1972 helix: 1.37 (0.14), residues: 1320 sheet: 0.68 (0.48), residues: 116 loop : -0.46 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 401 HIS 0.002 0.001 HIS A 475 PHE 0.013 0.001 PHE B 252 TYR 0.014 0.001 TYR B 531 ARG 0.001 0.000 ARG D 550 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 1016) hydrogen bonds : angle 3.82601 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00211 (17280) covalent geometry : angle 0.47664 (23152) *********************** 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 211 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.977 Fit side-chains REVERT: A 331 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 335 MET cc_start: 0.8365 (mmm) cc_final: 0.7905 (mmm) REVERT: A 424 MET cc_start: 0.9241 (tpp) cc_final: 0.8461 (tpp) REVERT: A 449 CYS cc_start: 0.8369 (p) cc_final: 0.7800 (p) REVERT: A 593 MET cc_start: 0.8240 (ttp) cc_final: 0.7969 (ttp) REVERT: B 304 THR cc_start: 0.9490 (m) cc_final: 0.9254 (p) REVERT: B 331 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7471 (mm-40) REVERT: B 335 MET cc_start: 0.8357 (mmm) cc_final: 0.7896 (mmm) REVERT: B 424 MET cc_start: 0.9258 (tpp) cc_final: 0.8524 (tpp) REVERT: B 449 CYS cc_start: 0.8322 (p) cc_final: 0.7754 (p) REVERT: B 494 LEU cc_start: 0.8908 (mt) cc_final: 0.8614 (mt) REVERT: B 593 MET cc_start: 0.8228 (ttp) cc_final: 0.7918 (ttp) REVERT: C 304 THR cc_start: 0.9488 (m) cc_final: 0.9253 (p) REVERT: C 331 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7461 (mm-40) REVERT: C 335 MET cc_start: 0.8356 (mmm) cc_final: 0.7894 (mmm) REVERT: C 449 CYS cc_start: 0.8324 (p) cc_final: 0.7755 (p) REVERT: C 593 MET cc_start: 0.8220 (ttp) cc_final: 0.7910 (ttp) REVERT: D 304 THR cc_start: 0.9486 (m) cc_final: 0.9252 (p) REVERT: D 331 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7468 (mm-40) REVERT: D 335 MET cc_start: 0.8368 (mmm) cc_final: 0.7908 (mmm) REVERT: D 424 MET cc_start: 0.9255 (tpp) cc_final: 0.8514 (tpp) REVERT: D 449 CYS cc_start: 0.8338 (p) cc_final: 0.7767 (p) REVERT: D 473 MET cc_start: 0.8893 (ttm) cc_final: 0.8622 (ttm) REVERT: D 494 LEU cc_start: 0.8905 (mt) cc_final: 0.8629 (mt) outliers start: 15 outliers final: 8 residues processed: 207 average time/residue: 0.2325 time to fit residues: 80.3968 Evaluate side-chains 172 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 195 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3553 r_free = 0.3553 target = 0.111608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087335 restraints weight = 30188.465| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.44 r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2236 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= 0.084 Angle : 0.459 8.470 23160 Z= 0.231 Chirality : 0.038 0.115 2492 Planarity : 0.003 0.031 2820 Dihedral : 9.468 58.947 2960 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1972 helix: 1.94 (0.14), residues: 1300 sheet: 0.70 (0.48), residues: 116 loop : -0.03 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 401 HIS 0.002 0.000 HIS A 475 PHE 0.012 0.001 PHE C 658 TYR 0.013 0.001 TYR A 531 ARG 0.001 0.000 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 1016) hydrogen bonds : angle 3.58731 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00170 (17280) covalent geometry : angle 0.45892 (23152) *********************** 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 213 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 2.053 Fit side-chains REVERT: A 303 ASP cc_start: 0.8419 (m-30) cc_final: 0.7987 (t0) REVERT: A 331 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 335 MET cc_start: 0.8310 (mmm) cc_final: 0.7846 (mmm) REVERT: A 449 CYS cc_start: 0.8157 (p) cc_final: 0.7577 (p) REVERT: A 538 MET cc_start: 0.8838 (mtm) cc_final: 0.8077 (mtm) REVERT: A 683 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8546 (m) REVERT: B 304 THR cc_start: 0.9479 (m) cc_final: 0.9253 (p) REVERT: B 331 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7351 (mm-40) REVERT: B 335 MET cc_start: 0.8314 (mmm) cc_final: 0.7830 (mmm) REVERT: B 449 CYS cc_start: 0.7983 (p) cc_final: 0.7542 (p) REVERT: B 538 MET cc_start: 0.8842 (mtm) cc_final: 0.8118 (mtm) REVERT: B 593 MET cc_start: 0.8311 (ttp) cc_final: 0.8101 (ttp) REVERT: B 683 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8554 (m) REVERT: C 304 THR cc_start: 0.9477 (m) cc_final: 0.9252 (p) REVERT: C 331 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7350 (mm-40) REVERT: C 335 MET cc_start: 0.8306 (mmm) cc_final: 0.7820 (mmm) REVERT: C 449 CYS cc_start: 0.7994 (p) cc_final: 0.7552 (p) REVERT: C 538 MET cc_start: 0.8840 (mtm) cc_final: 0.8120 (mtm) REVERT: C 593 MET cc_start: 0.8305 (ttp) cc_final: 0.8098 (ttp) REVERT: C 683 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8550 (m) REVERT: D 304 THR cc_start: 0.9476 (m) cc_final: 0.9252 (p) REVERT: D 331 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7342 (mm-40) REVERT: D 335 MET cc_start: 0.8327 (mmm) cc_final: 0.7845 (mmm) REVERT: D 449 CYS cc_start: 0.8024 (p) cc_final: 0.7577 (p) REVERT: D 473 MET cc_start: 0.8837 (ttm) cc_final: 0.8582 (ttm) REVERT: D 538 MET cc_start: 0.8823 (mtm) cc_final: 0.8105 (mtm) REVERT: D 683 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8543 (m) outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.2368 time to fit residues: 82.2441 Evaluate side-chains 184 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 683 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 475 HIS B 406 HIS B 475 HIS C 223 GLN C 406 HIS C 475 HIS D 406 HIS D 475 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083748 restraints weight = 30967.784| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.46 r_work: 0.2950 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17280 Z= 0.156 Angle : 0.509 9.194 23160 Z= 0.257 Chirality : 0.041 0.120 2492 Planarity : 0.003 0.041 2820 Dihedral : 9.516 58.666 2960 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.80 % Allowed : 9.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1972 helix: 2.16 (0.14), residues: 1304 sheet: 0.57 (0.47), residues: 116 loop : 0.09 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 401 HIS 0.003 0.001 HIS B 406 PHE 0.008 0.001 PHE C 658 TYR 0.016 0.001 TYR B 531 ARG 0.002 0.000 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 1016) hydrogen bonds : angle 3.60880 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00362 (17280) covalent geometry : angle 0.50952 (23152) *********************** 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 195 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 2.085 Fit side-chains REVERT: A 331 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7039 (mm-40) REVERT: A 335 MET cc_start: 0.8454 (mmm) cc_final: 0.7750 (mmm) REVERT: A 449 CYS cc_start: 0.8172 (p) cc_final: 0.7625 (p) REVERT: A 538 MET cc_start: 0.8962 (mtm) cc_final: 0.8472 (mtm) REVERT: B 269 MET cc_start: 0.9165 (tpp) cc_final: 0.8942 (tpp) REVERT: B 303 ASP cc_start: 0.8240 (m-30) cc_final: 0.7608 (t0) REVERT: B 331 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7028 (mm-40) REVERT: B 335 MET cc_start: 0.8451 (mmm) cc_final: 0.7748 (mmm) REVERT: B 449 CYS cc_start: 0.8110 (p) cc_final: 0.7575 (p) REVERT: B 538 MET cc_start: 0.8988 (mtm) cc_final: 0.8662 (mtp) REVERT: C 269 MET cc_start: 0.9167 (tpp) cc_final: 0.8946 (tpp) REVERT: C 303 ASP cc_start: 0.8237 (m-30) cc_final: 0.7611 (t0) REVERT: C 331 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7033 (mm-40) REVERT: C 335 MET cc_start: 0.8449 (mmm) cc_final: 0.7744 (mmm) REVERT: C 432 ASP cc_start: 0.8861 (t0) cc_final: 0.8635 (t0) REVERT: C 449 CYS cc_start: 0.8091 (p) cc_final: 0.7559 (p) REVERT: C 538 MET cc_start: 0.8980 (mtm) cc_final: 0.8436 (mtm) REVERT: D 269 MET cc_start: 0.9170 (tpp) cc_final: 0.8948 (tpp) REVERT: D 303 ASP cc_start: 0.8240 (m-30) cc_final: 0.7611 (t0) REVERT: D 331 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7033 (mm-40) REVERT: D 335 MET cc_start: 0.8452 (mmm) cc_final: 0.7751 (mmm) REVERT: D 449 CYS cc_start: 0.8204 (p) cc_final: 0.7682 (p) REVERT: D 473 MET cc_start: 0.8972 (ttm) cc_final: 0.8733 (ttm) REVERT: D 538 MET cc_start: 0.8967 (mtm) cc_final: 0.8418 (mtm) outliers start: 31 outliers final: 13 residues processed: 186 average time/residue: 0.2603 time to fit residues: 80.5410 Evaluate side-chains 170 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 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 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086170 restraints weight = 30694.717| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.45 r_work: 0.2993 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2475 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= 0.090 Angle : 0.458 8.359 23160 Z= 0.230 Chirality : 0.039 0.124 2492 Planarity : 0.003 0.038 2820 Dihedral : 9.078 58.057 2960 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.99 % Allowed : 10.29 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.20), residues: 1972 helix: 2.38 (0.15), residues: 1300 sheet: 0.77 (0.48), residues: 116 loop : 0.11 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 401 HIS 0.002 0.000 HIS A 406 PHE 0.007 0.001 PHE B 658 TYR 0.014 0.001 TYR A 531 ARG 0.001 0.000 ARG D 390 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1016) hydrogen bonds : angle 3.50178 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00195 (17280) covalent geometry : angle 0.45786 (23152) *********************** 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 197 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 2.049 Fit side-chains REVERT: A 303 ASP cc_start: 0.8431 (m-30) cc_final: 0.8095 (t0) REVERT: A 331 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7300 (mm-40) REVERT: A 335 MET cc_start: 0.8486 (mmm) cc_final: 0.7990 (mmm) REVERT: A 424 MET cc_start: 0.9235 (tpp) cc_final: 0.8894 (tpp) REVERT: A 449 CYS cc_start: 0.8069 (p) cc_final: 0.7500 (p) REVERT: A 538 MET cc_start: 0.8950 (mtm) cc_final: 0.8447 (mtm) REVERT: A 593 MET cc_start: 0.8602 (ttp) cc_final: 0.7487 (ttp) REVERT: B 269 MET cc_start: 0.9133 (tpp) cc_final: 0.8913 (tpp) REVERT: B 303 ASP cc_start: 0.8280 (m-30) cc_final: 0.7625 (t0) REVERT: B 331 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7294 (mm-40) REVERT: B 335 MET cc_start: 0.8488 (mmm) cc_final: 0.7996 (mmm) REVERT: B 424 MET cc_start: 0.9228 (tpp) cc_final: 0.8895 (tpp) REVERT: B 449 CYS cc_start: 0.8108 (p) cc_final: 0.7578 (p) REVERT: B 538 MET cc_start: 0.9014 (mtm) cc_final: 0.8610 (mtm) REVERT: B 593 MET cc_start: 0.8655 (ttp) cc_final: 0.7281 (ttp) REVERT: C 269 MET cc_start: 0.9128 (tpp) cc_final: 0.8910 (tpp) REVERT: C 303 ASP cc_start: 0.8275 (m-30) cc_final: 0.7624 (t0) REVERT: C 331 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7302 (mm-40) REVERT: C 335 MET cc_start: 0.8484 (mmm) cc_final: 0.7989 (mmm) REVERT: C 424 MET cc_start: 0.9237 (tpp) cc_final: 0.8900 (tpp) REVERT: C 449 CYS cc_start: 0.8085 (p) cc_final: 0.7559 (p) REVERT: C 538 MET cc_start: 0.8999 (mtm) cc_final: 0.8594 (mtm) REVERT: C 593 MET cc_start: 0.8660 (ttp) cc_final: 0.7280 (ttp) REVERT: D 269 MET cc_start: 0.9136 (tpp) cc_final: 0.8917 (tpp) REVERT: D 303 ASP cc_start: 0.8294 (m-30) cc_final: 0.7643 (t0) REVERT: D 331 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7293 (mm-40) REVERT: D 335 MET cc_start: 0.8492 (mmm) cc_final: 0.7998 (mmm) REVERT: D 424 MET cc_start: 0.9231 (tpp) cc_final: 0.8899 (tpp) REVERT: D 449 CYS cc_start: 0.8121 (p) cc_final: 0.7633 (p) REVERT: D 473 MET cc_start: 0.8910 (ttm) cc_final: 0.8667 (ttm) REVERT: D 538 MET cc_start: 0.8988 (mtm) cc_final: 0.8583 (mtm) REVERT: D 593 MET cc_start: 0.8130 (ttp) cc_final: 0.7885 (ttp) REVERT: D 595 LEU cc_start: 0.8498 (tp) cc_final: 0.8290 (tp) outliers start: 17 outliers final: 12 residues processed: 189 average time/residue: 0.2497 time to fit residues: 77.4771 Evaluate side-chains 177 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE 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 101 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 130 optimal weight: 0.0770 chunk 163 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086585 restraints weight = 30675.558| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.46 r_work: 0.3003 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17280 Z= 0.087 Angle : 0.466 8.163 23160 Z= 0.232 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.032 2820 Dihedral : 8.681 53.503 2960 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.99 % Allowed : 11.16 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1972 helix: 2.50 (0.15), residues: 1304 sheet: 0.91 (0.48), residues: 116 loop : 0.18 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 401 HIS 0.002 0.000 HIS A 256 PHE 0.008 0.001 PHE A 658 TYR 0.013 0.001 TYR A 531 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 1016) hydrogen bonds : angle 3.41647 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00184 (17280) covalent geometry : angle 0.46638 (23152) *********************** 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 206 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.768 Fit side-chains REVERT: A 269 MET cc_start: 0.9130 (tpp) cc_final: 0.8871 (tpp) REVERT: A 303 ASP cc_start: 0.8400 (m-30) cc_final: 0.7958 (t0) REVERT: A 331 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7318 (mm-40) REVERT: A 335 MET cc_start: 0.8405 (mmm) cc_final: 0.7912 (mmm) REVERT: A 424 MET cc_start: 0.9235 (tpp) cc_final: 0.8906 (tpp) REVERT: A 449 CYS cc_start: 0.8153 (p) cc_final: 0.7613 (p) REVERT: A 538 MET cc_start: 0.8948 (mtm) cc_final: 0.8581 (mtm) REVERT: A 593 MET cc_start: 0.8653 (ttp) cc_final: 0.7631 (ttp) REVERT: B 331 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7315 (mm-40) REVERT: B 335 MET cc_start: 0.8414 (mmm) cc_final: 0.7926 (mmm) REVERT: B 424 MET cc_start: 0.9219 (tpp) cc_final: 0.8881 (tpp) REVERT: B 449 CYS cc_start: 0.8057 (p) cc_final: 0.7535 (p) REVERT: B 538 MET cc_start: 0.9013 (mtm) cc_final: 0.8716 (mtm) REVERT: B 593 MET cc_start: 0.8572 (ttp) cc_final: 0.7206 (ttp) REVERT: C 303 ASP cc_start: 0.8240 (m-30) cc_final: 0.7986 (m-30) REVERT: C 331 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7316 (mm-40) REVERT: C 335 MET cc_start: 0.8413 (mmm) cc_final: 0.7922 (mmm) REVERT: C 424 MET cc_start: 0.9215 (tpp) cc_final: 0.8881 (tpp) REVERT: C 449 CYS cc_start: 0.8066 (p) cc_final: 0.7545 (p) REVERT: C 538 MET cc_start: 0.9010 (mtm) cc_final: 0.8698 (mtm) REVERT: C 593 MET cc_start: 0.8571 (ttp) cc_final: 0.7205 (ttp) REVERT: D 331 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7322 (mm-40) REVERT: D 335 MET cc_start: 0.8415 (mmm) cc_final: 0.7924 (mmm) REVERT: D 424 MET cc_start: 0.9220 (tpp) cc_final: 0.8886 (tpp) REVERT: D 449 CYS cc_start: 0.8102 (p) cc_final: 0.7572 (p) REVERT: D 473 MET cc_start: 0.8875 (ttm) cc_final: 0.8631 (ttm) REVERT: D 538 MET cc_start: 0.8987 (mtm) cc_final: 0.8674 (mtm) REVERT: D 593 MET cc_start: 0.8175 (ttp) cc_final: 0.7547 (tpp) outliers start: 17 outliers final: 9 residues processed: 197 average time/residue: 0.2185 time to fit residues: 71.8832 Evaluate side-chains 179 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 406 HIS A 475 HIS B 223 GLN B 406 HIS B 475 HIS C 223 GLN C 406 HIS C 475 HIS D 223 GLN D 475 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083147 restraints weight = 30758.451| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.45 r_work: 0.2942 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17280 Z= 0.158 Angle : 0.541 9.396 23160 Z= 0.265 Chirality : 0.041 0.116 2492 Planarity : 0.003 0.049 2820 Dihedral : 8.748 53.334 2960 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.28 % Allowed : 10.58 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.20), residues: 1972 helix: 2.47 (0.14), residues: 1304 sheet: 0.94 (0.48), residues: 116 loop : 0.18 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS B 406 PHE 0.008 0.001 PHE C 658 TYR 0.019 0.001 TYR B 531 ARG 0.002 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1016) hydrogen bonds : angle 3.51489 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00372 (17280) covalent geometry : angle 0.54078 (23152) *********************** 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 187 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 2.023 Fit side-chains REVERT: A 303 ASP cc_start: 0.8208 (m-30) cc_final: 0.7738 (t0) REVERT: A 331 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7088 (mm-40) REVERT: A 335 MET cc_start: 0.8385 (mmm) cc_final: 0.7734 (mmm) REVERT: A 424 MET cc_start: 0.9235 (tpp) cc_final: 0.8943 (tpp) REVERT: A 432 ASP cc_start: 0.8848 (t0) cc_final: 0.8645 (t0) REVERT: A 449 CYS cc_start: 0.8250 (p) cc_final: 0.7672 (p) REVERT: A 538 MET cc_start: 0.9029 (mtm) cc_final: 0.8782 (mtm) REVERT: A 593 MET cc_start: 0.8740 (ttp) cc_final: 0.7739 (ttp) REVERT: B 303 ASP cc_start: 0.8266 (m-30) cc_final: 0.8010 (m-30) REVERT: B 331 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7338 (mm-40) REVERT: B 335 MET cc_start: 0.8352 (mmm) cc_final: 0.7931 (mmm) REVERT: B 424 MET cc_start: 0.9215 (tpp) cc_final: 0.8921 (tpp) REVERT: B 432 ASP cc_start: 0.8858 (t0) cc_final: 0.8653 (t0) REVERT: B 449 CYS cc_start: 0.8287 (p) cc_final: 0.7792 (p) REVERT: B 538 MET cc_start: 0.9028 (mtm) cc_final: 0.8827 (mtm) REVERT: B 593 MET cc_start: 0.8648 (ttp) cc_final: 0.7327 (ttp) REVERT: C 303 ASP cc_start: 0.8293 (m-30) cc_final: 0.8062 (m-30) REVERT: C 331 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7348 (mm-40) REVERT: C 335 MET cc_start: 0.8346 (mmm) cc_final: 0.7922 (mmm) REVERT: C 424 MET cc_start: 0.9225 (tpp) cc_final: 0.8935 (tpp) REVERT: C 449 CYS cc_start: 0.8291 (p) cc_final: 0.7790 (p) REVERT: C 538 MET cc_start: 0.9018 (mtm) cc_final: 0.8800 (mtm) REVERT: C 593 MET cc_start: 0.8652 (ttp) cc_final: 0.7329 (ttp) REVERT: D 303 ASP cc_start: 0.8278 (m-30) cc_final: 0.8025 (m-30) REVERT: D 331 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7345 (mm-40) REVERT: D 335 MET cc_start: 0.8344 (mmm) cc_final: 0.7919 (mmm) REVERT: D 424 MET cc_start: 0.9216 (tpp) cc_final: 0.8928 (tpp) REVERT: D 432 ASP cc_start: 0.8855 (t0) cc_final: 0.8648 (t0) REVERT: D 449 CYS cc_start: 0.8303 (p) cc_final: 0.7801 (p) REVERT: D 538 MET cc_start: 0.9001 (mtm) cc_final: 0.8781 (mtm) outliers start: 22 outliers final: 11 residues processed: 178 average time/residue: 0.2287 time to fit residues: 68.2071 Evaluate side-chains 173 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 476 MET 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 406 HIS 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 112 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085303 restraints weight = 30808.048| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.46 r_work: 0.2982 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17280 Z= 0.092 Angle : 0.488 9.112 23160 Z= 0.237 Chirality : 0.039 0.114 2492 Planarity : 0.003 0.051 2820 Dihedral : 8.425 53.552 2960 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.64 % Allowed : 10.81 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.20), residues: 1972 helix: 2.57 (0.14), residues: 1304 sheet: 1.04 (0.48), residues: 116 loop : 0.21 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 401 HIS 0.002 0.001 HIS C 406 PHE 0.007 0.001 PHE A 658 TYR 0.015 0.001 TYR C 531 ARG 0.001 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 1016) hydrogen bonds : angle 3.42346 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00200 (17280) covalent geometry : angle 0.48763 (23152) *********************** 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 184 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 1.796 Fit side-chains REVERT: A 335 MET cc_start: 0.8307 (mmm) cc_final: 0.7639 (mmm) REVERT: A 424 MET cc_start: 0.9226 (tpp) cc_final: 0.8912 (tpp) REVERT: A 432 ASP cc_start: 0.8850 (t0) cc_final: 0.8645 (t0) REVERT: A 449 CYS cc_start: 0.8168 (p) cc_final: 0.7641 (p) REVERT: A 593 MET cc_start: 0.8680 (ttp) cc_final: 0.7688 (ttp) REVERT: B 269 MET cc_start: 0.9090 (tpp) cc_final: 0.8887 (tpp) REVERT: B 335 MET cc_start: 0.8310 (mmm) cc_final: 0.7645 (mmm) REVERT: B 424 MET cc_start: 0.9218 (tpp) cc_final: 0.8898 (tpp) REVERT: B 432 ASP cc_start: 0.8869 (t0) cc_final: 0.8655 (t0) REVERT: B 449 CYS cc_start: 0.8159 (p) cc_final: 0.7604 (p) REVERT: B 593 MET cc_start: 0.8557 (ttp) cc_final: 0.7186 (ttp) REVERT: C 269 MET cc_start: 0.9092 (tpp) cc_final: 0.8890 (tpp) REVERT: C 335 MET cc_start: 0.8303 (mmm) cc_final: 0.7640 (mmm) REVERT: C 424 MET cc_start: 0.9228 (tpp) cc_final: 0.8912 (tpp) REVERT: C 449 CYS cc_start: 0.8162 (p) cc_final: 0.7609 (p) REVERT: C 593 MET cc_start: 0.8556 (ttp) cc_final: 0.7174 (ttp) REVERT: D 269 MET cc_start: 0.9096 (tpp) cc_final: 0.8894 (tpp) REVERT: D 335 MET cc_start: 0.8308 (mmm) cc_final: 0.7639 (mmm) REVERT: D 424 MET cc_start: 0.9237 (tpp) cc_final: 0.8911 (tpp) REVERT: D 432 ASP cc_start: 0.8846 (t0) cc_final: 0.8633 (t0) REVERT: D 449 CYS cc_start: 0.8164 (p) cc_final: 0.7605 (p) REVERT: D 593 MET cc_start: 0.8118 (ttp) cc_final: 0.7568 (tpp) outliers start: 11 outliers final: 8 residues processed: 179 average time/residue: 0.2240 time to fit residues: 67.2310 Evaluate side-chains 174 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 222 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085142 restraints weight = 30830.123| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.47 r_work: 0.2979 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17280 Z= 0.100 Angle : 0.497 9.588 23160 Z= 0.241 Chirality : 0.039 0.117 2492 Planarity : 0.003 0.049 2820 Dihedral : 8.355 53.016 2960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.41 % Allowed : 11.40 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.20), residues: 1972 helix: 2.60 (0.14), residues: 1304 sheet: 1.05 (0.48), residues: 116 loop : 0.24 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 401 HIS 0.002 0.001 HIS C 406 PHE 0.007 0.001 PHE A 658 TYR 0.015 0.001 TYR B 531 ARG 0.002 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 1016) hydrogen bonds : angle 3.42200 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00226 (17280) covalent geometry : angle 0.49727 (23152) ********************** 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 178 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.881 Fit side-chains REVERT: A 269 MET cc_start: 0.9121 (tpp) cc_final: 0.8913 (tpp) REVERT: A 335 MET cc_start: 0.8166 (mmm) cc_final: 0.7524 (mmm) REVERT: A 424 MET cc_start: 0.9229 (tpp) cc_final: 0.8916 (tpp) REVERT: A 449 CYS cc_start: 0.8191 (p) cc_final: 0.7669 (p) REVERT: A 538 MET cc_start: 0.8851 (mtm) cc_final: 0.8529 (mtp) REVERT: A 593 MET cc_start: 0.8681 (ttp) cc_final: 0.7675 (ttp) REVERT: B 335 MET cc_start: 0.8165 (mmm) cc_final: 0.7526 (mmm) REVERT: B 424 MET cc_start: 0.9212 (tpp) cc_final: 0.8900 (tpp) REVERT: B 432 ASP cc_start: 0.8848 (t0) cc_final: 0.8647 (t0) REVERT: B 449 CYS cc_start: 0.8159 (p) cc_final: 0.7608 (p) REVERT: B 538 MET cc_start: 0.8871 (mtm) cc_final: 0.7994 (mtm) REVERT: B 593 MET cc_start: 0.8600 (ttp) cc_final: 0.7252 (ttp) REVERT: C 335 MET cc_start: 0.8162 (mmm) cc_final: 0.7523 (mmm) REVERT: C 424 MET cc_start: 0.9228 (tpp) cc_final: 0.8909 (tpp) REVERT: C 449 CYS cc_start: 0.8183 (p) cc_final: 0.7630 (p) REVERT: C 538 MET cc_start: 0.8847 (mtm) cc_final: 0.7970 (mtm) REVERT: C 593 MET cc_start: 0.8600 (ttp) cc_final: 0.7244 (ttp) REVERT: D 335 MET cc_start: 0.8168 (mmm) cc_final: 0.7525 (mmm) REVERT: D 424 MET cc_start: 0.9235 (tpp) cc_final: 0.8926 (tpp) REVERT: D 432 ASP cc_start: 0.8827 (t0) cc_final: 0.8624 (t0) REVERT: D 449 CYS cc_start: 0.8202 (p) cc_final: 0.7654 (p) REVERT: D 538 MET cc_start: 0.8834 (mtm) cc_final: 0.7949 (mtm) outliers start: 7 outliers final: 4 residues processed: 175 average time/residue: 0.2348 time to fit residues: 68.0767 Evaluate side-chains 169 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 135 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.0670 chunk 123 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.110653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085889 restraints weight = 30592.686| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.46 r_work: 0.2994 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17280 Z= 0.092 Angle : 0.498 10.762 23160 Z= 0.240 Chirality : 0.039 0.168 2492 Planarity : 0.003 0.047 2820 Dihedral : 8.252 54.628 2960 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.23 % Allowed : 11.80 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.20), residues: 1972 helix: 2.64 (0.14), residues: 1304 sheet: 1.11 (0.48), residues: 116 loop : 0.25 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.000 HIS C 406 PHE 0.007 0.001 PHE A 658 TYR 0.014 0.001 TYR C 531 ARG 0.002 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 1016) hydrogen bonds : angle 3.39831 ( 2976) SS BOND : angle 0.00000 ( 8) covalent geometry : bond 0.00200 (17280) covalent geometry : angle 0.49807 (23152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7341.10 seconds wall clock time: 128 minutes 52.49 seconds (7732.49 seconds total)