Starting phenix.real_space_refine on Thu Sep 18 14:43:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gyn_0093/09_2025/6gyn_0093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gyn_0093/09_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_0093/09_2025/6gyn_0093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2025/6gyn_0093.map" model { file = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2025/6gyn_0093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gyn_0093/09_2025/6gyn_0093.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 132 5.16 5 C 11148 2.51 5 N 2684 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 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-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C Time building chain proxies: 5.54, per 1000 atoms: 0.33 Number of scatterers: 16932 At special positions: 0 Unit cell: (132.66, 132.66, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 16 15.00 O 2952 8.00 N 2684 7.00 C 11148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 429 " distance=0.00 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 434 " distance=0.00 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 449 " distance=0.00 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 478 " distance=0.00 Simple disulfide: pdb=" SG CYS C 505 " - pdb=" SG CYS C 505 " distance=0.00 Simple disulfide: pdb=" SG CYS C 586 " - pdb=" SG CYS C 586 " distance=0.00 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 662 " distance=0.00 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 679 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 677.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 70.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 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: 3.07 Time building geometry restraints manager: 1.95 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: 0.01 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.15), residues: 1972 helix: -1.78 (0.11), residues: 1312 sheet: 0.54 (0.48), residues: 116 loop : -1.46 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 396 TYR 0.032 0.003 TYR C 633 PHE 0.024 0.002 PHE B 379 TRP 0.022 0.003 TRP A 401 HIS 0.010 0.002 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00801 (17280) covalent geometry : angle 0.84944 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.14292 ( 1016) hydrogen bonds : angle 5.95152 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.534 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: 0.8773 (tt) REVERT: B 331 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 335 MET cc_start: 0.8080 (mmm) cc_final: 0.7592 (mmm) REVERT: B 407 MET cc_start: 0.8465 (tpp) cc_final: 0.8168 (tpt) REVERT: B 432 ASP cc_start: 0.8657 (t70) cc_final: 0.8359 (t70) REVERT: B 449 CYS cc_start: 0.8414 (p) cc_final: 0.8123 (p) REVERT: C 308 ILE cc_start: 0.8972 (mt) cc_final: 0.8771 (tt) REVERT: C 331 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7456 (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: 0.8167 (tpt) REVERT: C 432 ASP cc_start: 0.8655 (t70) cc_final: 0.8355 (t70) REVERT: C 449 CYS cc_start: 0.8407 (p) cc_final: 0.8121 (p) REVERT: D 308 ILE cc_start: 0.8974 (mt) cc_final: 0.8771 (tt) REVERT: D 331 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7455 (mm-40) REVERT: D 335 MET cc_start: 0.8087 (mmm) cc_final: 0.7599 (mmm) REVERT: D 407 MET cc_start: 0.8461 (tpp) cc_final: 0.8165 (tpt) REVERT: D 432 ASP cc_start: 0.8652 (t70) cc_final: 0.8356 (t70) REVERT: D 449 CYS cc_start: 0.8400 (p) cc_final: 0.8127 (p) REVERT: D 473 MET cc_start: 0.8524 (ttm) cc_final: 0.8233 (ttm) REVERT: D 593 MET cc_start: 0.8534 (ttt) cc_final: 0.8333 (ttt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1398 time to fit residues: 63.6105 Evaluate side-chains 162 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 459 ASN A 541 HIS A 602 ASN B 406 HIS B 459 ASN B 541 HIS C 406 HIS C 459 ASN C 541 HIS C 602 ASN D 406 HIS D 459 ASN D 541 HIS D 602 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086007 restraints weight = 30327.645| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.44 r_work: 0.2988 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17280 Z= 0.111 Angle : 0.512 6.842 23160 Z= 0.263 Chirality : 0.041 0.167 2492 Planarity : 0.004 0.034 2820 Dihedral : 10.092 69.474 2960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.76 % Allowed : 8.78 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.18), residues: 1972 helix: 0.48 (0.13), residues: 1340 sheet: 0.77 (0.48), residues: 116 loop : -0.92 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 550 TYR 0.014 0.001 TYR C 531 PHE 0.010 0.001 PHE C 689 TRP 0.018 0.001 TRP A 401 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00239 (17280) covalent geometry : angle 0.51223 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03730 ( 1016) hydrogen bonds : angle 4.11525 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.670 Fit side-chains REVERT: A 214 MET cc_start: 0.6602 (mtt) cc_final: 0.6291 (mmm) REVERT: A 269 MET cc_start: 0.8587 (mmm) cc_final: 0.8079 (tpp) REVERT: A 304 THR cc_start: 0.9509 (m) cc_final: 0.9288 (p) REVERT: A 331 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7416 (mm-40) REVERT: A 335 MET cc_start: 0.8328 (mmm) cc_final: 0.7872 (mmm) REVERT: B 214 MET cc_start: 0.6623 (mtt) cc_final: 0.6275 (mmm) REVERT: B 304 THR cc_start: 0.9412 (m) cc_final: 0.9199 (p) REVERT: B 331 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7472 (mm-40) REVERT: B 335 MET cc_start: 0.8335 (mmm) cc_final: 0.7881 (mmm) REVERT: B 449 CYS cc_start: 0.8183 (p) cc_final: 0.7731 (p) REVERT: C 214 MET cc_start: 0.6643 (mtt) cc_final: 0.6279 (mmm) REVERT: C 304 THR cc_start: 0.9412 (m) cc_final: 0.9199 (p) REVERT: C 331 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7465 (mm-40) REVERT: C 335 MET cc_start: 0.8322 (mmm) cc_final: 0.7868 (mmm) REVERT: C 449 CYS cc_start: 0.8189 (p) cc_final: 0.7737 (p) REVERT: D 214 MET cc_start: 0.6607 (mtt) cc_final: 0.6284 (mmm) REVERT: D 304 THR cc_start: 0.9411 (m) cc_final: 0.9200 (p) REVERT: D 331 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7466 (mm-40) REVERT: D 335 MET cc_start: 0.8334 (mmm) cc_final: 0.7881 (mmm) REVERT: D 449 CYS cc_start: 0.8189 (p) cc_final: 0.7738 (p) REVERT: D 473 MET cc_start: 0.8889 (ttm) cc_final: 0.8623 (ttm) outliers start: 13 outliers final: 4 residues processed: 230 average time/residue: 0.1151 time to fit residues: 42.6715 Evaluate side-chains 179 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 187 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085881 restraints weight = 30926.621| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.46 r_work: 0.2992 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1946 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= 0.099 Angle : 0.472 5.733 23160 Z= 0.242 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.662 62.364 2960 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.47 % Allowed : 10.47 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 1972 helix: 1.51 (0.14), residues: 1296 sheet: 0.94 (0.49), residues: 116 loop : -0.48 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 390 TYR 0.013 0.001 TYR B 531 PHE 0.012 0.001 PHE B 252 TRP 0.017 0.001 TRP A 401 HIS 0.002 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00218 (17280) covalent geometry : angle 0.47183 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03257 ( 1016) hydrogen bonds : angle 3.80405 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.754 Fit side-chains REVERT: A 269 MET cc_start: 0.8725 (mmm) cc_final: 0.8068 (tpp) REVERT: A 331 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7459 (mm-40) REVERT: A 335 MET cc_start: 0.8310 (mmm) cc_final: 0.7857 (mmm) REVERT: A 449 CYS cc_start: 0.8342 (p) cc_final: 0.7791 (p) REVERT: A 593 MET cc_start: 0.8184 (ttp) cc_final: 0.7902 (ttp) REVERT: B 304 THR cc_start: 0.9489 (m) cc_final: 0.9250 (p) REVERT: B 331 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7464 (mm-40) REVERT: B 335 MET cc_start: 0.8313 (mmm) cc_final: 0.7860 (mmm) REVERT: B 449 CYS cc_start: 0.8253 (p) cc_final: 0.7657 (p) REVERT: B 494 LEU cc_start: 0.8914 (mt) cc_final: 0.8627 (mt) REVERT: B 593 MET cc_start: 0.8195 (ttp) cc_final: 0.7879 (ttp) REVERT: C 304 THR cc_start: 0.9488 (m) cc_final: 0.9250 (p) REVERT: C 331 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7458 (mm-40) REVERT: C 335 MET cc_start: 0.8306 (mmm) cc_final: 0.7855 (mmm) REVERT: C 449 CYS cc_start: 0.8261 (p) cc_final: 0.7663 (p) REVERT: C 494 LEU cc_start: 0.8916 (mt) cc_final: 0.8625 (mt) REVERT: C 593 MET cc_start: 0.8179 (ttp) cc_final: 0.7871 (ttp) REVERT: D 304 THR cc_start: 0.9489 (m) cc_final: 0.9252 (p) REVERT: D 331 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7449 (mm-40) REVERT: D 335 MET cc_start: 0.8318 (mmm) cc_final: 0.7868 (mmm) REVERT: D 449 CYS cc_start: 0.8271 (p) cc_final: 0.7668 (p) REVERT: D 473 MET cc_start: 0.8892 (ttm) cc_final: 0.8636 (ttm) REVERT: D 494 LEU cc_start: 0.8909 (mt) cc_final: 0.8625 (mt) REVERT: D 593 MET cc_start: 0.8160 (ttp) cc_final: 0.7831 (ttp) outliers start: 8 outliers final: 4 residues processed: 207 average time/residue: 0.1024 time to fit residues: 36.0935 Evaluate side-chains 171 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 2.9990 chunk 163 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086033 restraints weight = 30667.163| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.46 r_work: 0.2993 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2172 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= 0.096 Angle : 0.475 8.019 23160 Z= 0.237 Chirality : 0.039 0.113 2492 Planarity : 0.003 0.030 2820 Dihedral : 9.348 55.456 2960 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.10 % Allowed : 10.29 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.19), residues: 1972 helix: 1.96 (0.14), residues: 1300 sheet: 0.87 (0.49), residues: 116 loop : -0.19 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 390 TYR 0.014 0.001 TYR B 531 PHE 0.006 0.001 PHE B 658 TRP 0.016 0.001 TRP A 401 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00210 (17280) covalent geometry : angle 0.47463 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03066 ( 1016) hydrogen bonds : angle 3.61742 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.712 Fit side-chains REVERT: A 331 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7358 (mm-40) REVERT: A 335 MET cc_start: 0.8348 (mmm) cc_final: 0.7896 (mmm) REVERT: A 424 MET cc_start: 0.9262 (tpp) cc_final: 0.8391 (tpp) REVERT: A 449 CYS cc_start: 0.8294 (p) cc_final: 0.7721 (p) REVERT: A 538 MET cc_start: 0.8877 (mtm) cc_final: 0.8150 (mtm) REVERT: B 304 THR cc_start: 0.9493 (m) cc_final: 0.9269 (p) REVERT: B 331 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7424 (mm-40) REVERT: B 335 MET cc_start: 0.8323 (mmm) cc_final: 0.7868 (mmm) REVERT: B 424 MET cc_start: 0.9251 (tpp) cc_final: 0.8379 (tpp) REVERT: B 449 CYS cc_start: 0.8248 (p) cc_final: 0.7656 (p) REVERT: B 538 MET cc_start: 0.8879 (mtm) cc_final: 0.8486 (mtm) REVERT: B 593 MET cc_start: 0.8298 (ttp) cc_final: 0.8085 (ttp) REVERT: C 304 THR cc_start: 0.9494 (m) cc_final: 0.9271 (p) REVERT: C 331 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7416 (mm-40) REVERT: C 335 MET cc_start: 0.8311 (mmm) cc_final: 0.7854 (mmm) REVERT: C 424 MET cc_start: 0.9266 (tpp) cc_final: 0.8398 (tpp) REVERT: C 449 CYS cc_start: 0.8234 (p) cc_final: 0.7647 (p) REVERT: C 538 MET cc_start: 0.8878 (mtm) cc_final: 0.8555 (mtm) REVERT: C 593 MET cc_start: 0.8291 (ttp) cc_final: 0.8073 (ttp) REVERT: D 304 THR cc_start: 0.9497 (m) cc_final: 0.9276 (p) REVERT: D 331 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7417 (mm-40) REVERT: D 335 MET cc_start: 0.8320 (mmm) cc_final: 0.7864 (mmm) REVERT: D 424 MET cc_start: 0.9285 (tpp) cc_final: 0.8452 (tpp) REVERT: D 449 CYS cc_start: 0.8238 (p) cc_final: 0.7643 (p) REVERT: D 473 MET cc_start: 0.8845 (ttm) cc_final: 0.8582 (ttm) REVERT: D 538 MET cc_start: 0.8873 (mtm) cc_final: 0.8472 (mtm) REVERT: D 593 MET cc_start: 0.8384 (ttp) cc_final: 0.8156 (ttp) outliers start: 19 outliers final: 8 residues processed: 207 average time/residue: 0.1055 time to fit residues: 36.4853 Evaluate side-chains 181 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 164 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 87 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.108853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084271 restraints weight = 30726.595| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.42 r_work: 0.2959 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17280 Z= 0.139 Angle : 0.495 8.941 23160 Z= 0.251 Chirality : 0.041 0.129 2492 Planarity : 0.003 0.029 2820 Dihedral : 9.243 58.043 2960 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.63 % Allowed : 9.36 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.19), residues: 1972 helix: 2.19 (0.14), residues: 1304 sheet: 0.84 (0.49), residues: 116 loop : -0.02 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.016 0.001 TYR A 531 PHE 0.006 0.001 PHE B 658 TRP 0.017 0.001 TRP A 401 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00322 (17280) covalent geometry : angle 0.49486 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03249 ( 1016) hydrogen bonds : angle 3.63558 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.636 Fit side-chains REVERT: A 331 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7270 (mm-40) REVERT: A 335 MET cc_start: 0.8300 (mmm) cc_final: 0.7858 (mmm) REVERT: A 424 MET cc_start: 0.9266 (tpp) cc_final: 0.8923 (tpp) REVERT: A 449 CYS cc_start: 0.8311 (p) cc_final: 0.7709 (p) REVERT: A 538 MET cc_start: 0.8930 (mtm) cc_final: 0.8438 (mtm) REVERT: B 304 THR cc_start: 0.9465 (m) cc_final: 0.9255 (p) REVERT: B 331 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7257 (mm-40) REVERT: B 335 MET cc_start: 0.8463 (mmm) cc_final: 0.7979 (mmm) REVERT: B 424 MET cc_start: 0.9251 (tpp) cc_final: 0.8889 (tpp) REVERT: B 538 MET cc_start: 0.8969 (mtm) cc_final: 0.8432 (mtm) REVERT: C 304 THR cc_start: 0.9465 (m) cc_final: 0.9255 (p) REVERT: C 331 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7274 (mm-40) REVERT: C 335 MET cc_start: 0.8458 (mmm) cc_final: 0.7975 (mmm) REVERT: C 538 MET cc_start: 0.8944 (mtm) cc_final: 0.8562 (mtm) REVERT: D 304 THR cc_start: 0.9467 (m) cc_final: 0.9259 (p) REVERT: D 331 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7265 (mm-40) REVERT: D 335 MET cc_start: 0.8464 (mmm) cc_final: 0.7981 (mmm) REVERT: D 473 MET cc_start: 0.8904 (ttm) cc_final: 0.8656 (ttm) REVERT: D 538 MET cc_start: 0.8937 (mtm) cc_final: 0.8546 (mtm) outliers start: 28 outliers final: 16 residues processed: 182 average time/residue: 0.1034 time to fit residues: 31.3821 Evaluate side-chains 175 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 126 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS C 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084630 restraints weight = 30814.403| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.44 r_work: 0.2964 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17280 Z= 0.116 Angle : 0.481 8.526 23160 Z= 0.241 Chirality : 0.040 0.116 2492 Planarity : 0.003 0.029 2820 Dihedral : 9.109 59.990 2960 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.28 % Allowed : 10.35 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.20), residues: 1972 helix: 2.32 (0.14), residues: 1304 sheet: 0.88 (0.49), residues: 116 loop : 0.10 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 387 TYR 0.015 0.001 TYR A 531 PHE 0.011 0.001 PHE B 658 TRP 0.016 0.001 TRP A 401 HIS 0.002 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00266 (17280) covalent geometry : angle 0.48134 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03126 ( 1016) hydrogen bonds : angle 3.53117 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.518 Fit side-chains REVERT: A 331 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7269 (mm-40) REVERT: A 335 MET cc_start: 0.8509 (mmm) cc_final: 0.8024 (mmm) REVERT: A 449 CYS cc_start: 0.8092 (p) cc_final: 0.7523 (p) REVERT: A 538 MET cc_start: 0.8889 (mtm) cc_final: 0.8418 (mtm) REVERT: A 593 MET cc_start: 0.8670 (ttp) cc_final: 0.7518 (ttp) REVERT: B 304 THR cc_start: 0.9461 (m) cc_final: 0.9252 (p) REVERT: B 331 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7264 (mm-40) REVERT: B 335 MET cc_start: 0.8506 (mmm) cc_final: 0.8017 (mmm) REVERT: B 538 MET cc_start: 0.8964 (mtm) cc_final: 0.8346 (mtm) REVERT: B 593 MET cc_start: 0.8688 (ttp) cc_final: 0.7371 (ttp) REVERT: C 304 THR cc_start: 0.9460 (m) cc_final: 0.9251 (p) REVERT: C 331 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7271 (mm-40) REVERT: C 335 MET cc_start: 0.8468 (mmm) cc_final: 0.8003 (mmm) REVERT: C 538 MET cc_start: 0.9033 (mtm) cc_final: 0.8722 (mtm) REVERT: C 593 MET cc_start: 0.8688 (ttp) cc_final: 0.7363 (ttp) REVERT: D 304 THR cc_start: 0.9463 (m) cc_final: 0.9255 (p) REVERT: D 331 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7265 (mm-40) REVERT: D 335 MET cc_start: 0.8478 (mmm) cc_final: 0.8015 (mmm) REVERT: D 473 MET cc_start: 0.8919 (ttm) cc_final: 0.8673 (ttm) REVERT: D 538 MET cc_start: 0.8991 (mtm) cc_final: 0.8631 (mtm) REVERT: D 593 MET cc_start: 0.8699 (ttp) cc_final: 0.7446 (ttp) outliers start: 22 outliers final: 16 residues processed: 185 average time/residue: 0.0946 time to fit residues: 29.3577 Evaluate side-chains 186 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN C 223 GLN C 475 HIS D 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084756 restraints weight = 30717.445| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.42 r_work: 0.2968 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17280 Z= 0.111 Angle : 0.476 8.357 23160 Z= 0.237 Chirality : 0.039 0.117 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.953 58.777 2960 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.40 % Allowed : 10.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.20), residues: 1972 helix: 2.48 (0.14), residues: 1304 sheet: 1.01 (0.49), residues: 116 loop : 0.21 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 387 TYR 0.014 0.001 TYR C 531 PHE 0.009 0.001 PHE A 658 TRP 0.015 0.001 TRP C 401 HIS 0.002 0.001 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.00252 (17280) covalent geometry : angle 0.47575 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03063 ( 1016) hydrogen bonds : angle 3.46232 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.671 Fit side-chains REVERT: A 331 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7281 (mm-40) REVERT: A 335 MET cc_start: 0.8379 (mmm) cc_final: 0.7928 (mmm) REVERT: A 424 MET cc_start: 0.9211 (tpp) cc_final: 0.8384 (tpp) REVERT: A 432 ASP cc_start: 0.8851 (t0) cc_final: 0.8627 (t0) REVERT: A 449 CYS cc_start: 0.8061 (p) cc_final: 0.7481 (p) REVERT: A 538 MET cc_start: 0.8944 (mtm) cc_final: 0.8737 (mtm) REVERT: A 593 MET cc_start: 0.8632 (ttp) cc_final: 0.7526 (ttp) REVERT: B 331 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7278 (mm-40) REVERT: B 335 MET cc_start: 0.8432 (mmm) cc_final: 0.7961 (mmm) REVERT: B 424 MET cc_start: 0.9196 (tpp) cc_final: 0.8354 (tpp) REVERT: B 432 ASP cc_start: 0.8852 (t0) cc_final: 0.8624 (t0) REVERT: B 593 MET cc_start: 0.8668 (ttp) cc_final: 0.7414 (ttp) REVERT: C 331 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7284 (mm-40) REVERT: C 335 MET cc_start: 0.8426 (mmm) cc_final: 0.7954 (mmm) REVERT: C 424 MET cc_start: 0.9215 (tpp) cc_final: 0.8475 (tpp) REVERT: C 538 MET cc_start: 0.9014 (mtm) cc_final: 0.8778 (mtm) REVERT: C 575 GLU cc_start: 0.8264 (tp30) cc_final: 0.8024 (tp30) REVERT: C 593 MET cc_start: 0.8669 (ttp) cc_final: 0.7409 (ttp) REVERT: D 331 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7281 (mm-40) REVERT: D 335 MET cc_start: 0.8430 (mmm) cc_final: 0.7956 (mmm) REVERT: D 424 MET cc_start: 0.9212 (tpp) cc_final: 0.8472 (tpp) REVERT: D 432 ASP cc_start: 0.8879 (t0) cc_final: 0.8649 (t0) REVERT: D 473 MET cc_start: 0.8982 (ttm) cc_final: 0.8762 (ttm) REVERT: D 538 MET cc_start: 0.9005 (mtm) cc_final: 0.8741 (mtm) REVERT: D 575 GLU cc_start: 0.8252 (tp30) cc_final: 0.8012 (tp30) REVERT: D 593 MET cc_start: 0.8696 (ttp) cc_final: 0.7507 (ttp) outliers start: 24 outliers final: 12 residues processed: 179 average time/residue: 0.0937 time to fit residues: 28.3689 Evaluate side-chains 179 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 26 optimal weight: 0.0770 chunk 126 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 223 GLN B 475 HIS C 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082486 restraints weight = 31236.051| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.43 r_work: 0.2930 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17280 Z= 0.166 Angle : 0.518 7.440 23160 Z= 0.260 Chirality : 0.041 0.117 2492 Planarity : 0.003 0.028 2820 Dihedral : 9.005 53.659 2960 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.16 % Allowed : 10.23 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.20), residues: 1972 helix: 2.44 (0.14), residues: 1304 sheet: 1.01 (0.49), residues: 116 loop : 0.17 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.016 0.002 TYR D 531 PHE 0.008 0.001 PHE A 658 TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00388 (17280) covalent geometry : angle 0.51772 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03330 ( 1016) hydrogen bonds : angle 3.52992 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.618 Fit side-chains REVERT: A 303 ASP cc_start: 0.8482 (m-30) cc_final: 0.8111 (t0) REVERT: A 331 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7041 (mm-40) REVERT: A 335 MET cc_start: 0.8343 (mmm) cc_final: 0.7709 (mmm) REVERT: A 432 ASP cc_start: 0.8849 (t0) cc_final: 0.8633 (t0) REVERT: A 449 CYS cc_start: 0.8247 (p) cc_final: 0.7675 (p) REVERT: A 538 MET cc_start: 0.9010 (mtm) cc_final: 0.8766 (mtm) REVERT: A 593 MET cc_start: 0.8692 (ttp) cc_final: 0.7593 (ttp) REVERT: B 331 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7297 (mm-40) REVERT: B 335 MET cc_start: 0.8330 (mmm) cc_final: 0.7908 (mmm) REVERT: B 432 ASP cc_start: 0.8858 (t0) cc_final: 0.8638 (t0) REVERT: B 538 MET cc_start: 0.8840 (mtm) cc_final: 0.8216 (mtm) REVERT: B 593 MET cc_start: 0.8701 (ttp) cc_final: 0.7434 (ttp) REVERT: C 331 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7301 (mm-40) REVERT: C 335 MET cc_start: 0.8330 (mmm) cc_final: 0.7908 (mmm) REVERT: C 424 MET cc_start: 0.9200 (tpp) cc_final: 0.8945 (tpp) REVERT: C 593 MET cc_start: 0.8706 (ttp) cc_final: 0.7435 (ttp) REVERT: D 331 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7292 (mm-40) REVERT: D 335 MET cc_start: 0.8334 (mmm) cc_final: 0.7912 (mmm) REVERT: D 424 MET cc_start: 0.9236 (tpp) cc_final: 0.8996 (tpp) REVERT: D 432 ASP cc_start: 0.8885 (t0) cc_final: 0.8665 (t0) REVERT: D 473 MET cc_start: 0.8973 (ttm) cc_final: 0.8755 (ttm) REVERT: D 538 MET cc_start: 0.8987 (mtm) cc_final: 0.8780 (mtm) REVERT: D 593 MET cc_start: 0.8701 (ttp) cc_final: 0.7489 (ttp) outliers start: 20 outliers final: 13 residues processed: 163 average time/residue: 0.1056 time to fit residues: 29.0144 Evaluate side-chains 166 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.108266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083524 restraints weight = 30921.579| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.43 r_work: 0.2947 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17280 Z= 0.125 Angle : 0.498 9.560 23160 Z= 0.248 Chirality : 0.040 0.116 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.771 53.985 2960 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.05 % Allowed : 10.52 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.20), residues: 1972 helix: 2.48 (0.14), residues: 1308 sheet: 1.03 (0.49), residues: 116 loop : 0.19 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 378 TYR 0.017 0.001 TYR B 531 PHE 0.007 0.001 PHE D 658 TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00288 (17280) covalent geometry : angle 0.49812 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03124 ( 1016) hydrogen bonds : angle 3.47640 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.685 Fit side-chains REVERT: A 335 MET cc_start: 0.8326 (mmm) cc_final: 0.7668 (mmm) REVERT: A 424 MET cc_start: 0.9201 (tpp) cc_final: 0.8457 (tpp) REVERT: A 432 ASP cc_start: 0.8866 (t0) cc_final: 0.8650 (t0) REVERT: A 449 CYS cc_start: 0.8160 (p) cc_final: 0.7573 (p) REVERT: A 538 MET cc_start: 0.8991 (mtm) cc_final: 0.8786 (mtm) REVERT: A 563 MET cc_start: 0.9106 (tpp) cc_final: 0.8766 (tpt) REVERT: A 593 MET cc_start: 0.8640 (ttp) cc_final: 0.7421 (ttp) REVERT: B 335 MET cc_start: 0.8321 (mmm) cc_final: 0.7668 (mmm) REVERT: B 424 MET cc_start: 0.9190 (tpp) cc_final: 0.8441 (tpp) REVERT: B 432 ASP cc_start: 0.8860 (t0) cc_final: 0.8642 (t0) REVERT: B 538 MET cc_start: 0.8882 (mtm) cc_final: 0.8230 (mtm) REVERT: B 563 MET cc_start: 0.9122 (tpp) cc_final: 0.8776 (tpt) REVERT: B 593 MET cc_start: 0.8632 (ttp) cc_final: 0.7289 (ttp) REVERT: C 335 MET cc_start: 0.8317 (mmm) cc_final: 0.7660 (mmm) REVERT: C 424 MET cc_start: 0.9219 (tpp) cc_final: 0.8490 (tpp) REVERT: C 538 MET cc_start: 0.8871 (mtm) cc_final: 0.8257 (mtm) REVERT: C 593 MET cc_start: 0.8639 (ttp) cc_final: 0.7293 (ttp) REVERT: D 335 MET cc_start: 0.8322 (mmm) cc_final: 0.7668 (mmm) REVERT: D 424 MET cc_start: 0.9221 (tpp) cc_final: 0.8946 (tpp) REVERT: D 432 ASP cc_start: 0.8844 (t0) cc_final: 0.8615 (t0) REVERT: D 473 MET cc_start: 0.8974 (ttm) cc_final: 0.8754 (ttm) REVERT: D 593 MET cc_start: 0.8669 (ttp) cc_final: 0.7380 (ttp) outliers start: 18 outliers final: 15 residues processed: 179 average time/residue: 0.0994 time to fit residues: 29.6697 Evaluate side-chains 175 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 476 MET 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 456 MET Chi-restraints excluded: chain C residue 476 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 476 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 137 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 0.0050 chunk 110 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085315 restraints weight = 30556.342| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.41 r_work: 0.2979 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2750 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= 0.094 Angle : 0.496 12.039 23160 Z= 0.243 Chirality : 0.039 0.114 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.470 54.221 2960 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.99 % Allowed : 10.76 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.20), residues: 1972 helix: 2.59 (0.14), residues: 1308 sheet: 1.09 (0.49), residues: 116 loop : 0.21 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 378 TYR 0.015 0.001 TYR B 531 PHE 0.007 0.001 PHE D 658 TRP 0.015 0.001 TRP B 401 HIS 0.002 0.000 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00204 (17280) covalent geometry : angle 0.49591 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.02934 ( 1016) hydrogen bonds : angle 3.41816 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.623 Fit side-chains REVERT: A 269 MET cc_start: 0.9045 (tpp) cc_final: 0.8333 (tpp) REVERT: A 335 MET cc_start: 0.8170 (mmm) cc_final: 0.7527 (mmm) REVERT: A 424 MET cc_start: 0.9205 (tpp) cc_final: 0.8487 (tpp) REVERT: A 432 ASP cc_start: 0.8859 (t0) cc_final: 0.8643 (t0) REVERT: A 449 CYS cc_start: 0.8174 (p) cc_final: 0.7653 (p) REVERT: A 538 MET cc_start: 0.8927 (mtm) cc_final: 0.8697 (mtm) REVERT: A 593 MET cc_start: 0.8668 (ttp) cc_final: 0.7595 (ttp) REVERT: B 335 MET cc_start: 0.8163 (mmm) cc_final: 0.7527 (mmm) REVERT: B 424 MET cc_start: 0.9187 (tpp) cc_final: 0.8459 (tpp) REVERT: B 432 ASP cc_start: 0.8878 (t0) cc_final: 0.8660 (t0) REVERT: B 538 MET cc_start: 0.8854 (mtm) cc_final: 0.8555 (mtp) REVERT: B 593 MET cc_start: 0.8606 (ttp) cc_final: 0.7267 (ttp) REVERT: C 335 MET cc_start: 0.8156 (mmm) cc_final: 0.7513 (mmm) REVERT: C 424 MET cc_start: 0.9212 (tpp) cc_final: 0.8463 (tpp) REVERT: C 538 MET cc_start: 0.8824 (mtm) cc_final: 0.8185 (mtm) REVERT: C 593 MET cc_start: 0.8612 (ttp) cc_final: 0.7275 (ttp) REVERT: D 335 MET cc_start: 0.8167 (mmm) cc_final: 0.7530 (mmm) REVERT: D 424 MET cc_start: 0.9210 (tpp) cc_final: 0.8916 (tpp) REVERT: D 432 ASP cc_start: 0.8846 (t0) cc_final: 0.8616 (t0) REVERT: D 473 MET cc_start: 0.8950 (ttm) cc_final: 0.8727 (ttm) REVERT: D 538 MET cc_start: 0.8806 (mtm) cc_final: 0.8494 (mtp) REVERT: D 593 MET cc_start: 0.8635 (ttp) cc_final: 0.7358 (ttp) outliers start: 17 outliers final: 6 residues processed: 193 average time/residue: 0.1123 time to fit residues: 35.6863 Evaluate side-chains 177 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 158 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.108456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083766 restraints weight = 30670.798| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.42 r_work: 0.2956 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17280 Z= 0.134 Angle : 0.535 10.655 23160 Z= 0.261 Chirality : 0.041 0.157 2492 Planarity : 0.003 0.055 2820 Dihedral : 8.552 53.540 2960 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.70 % Allowed : 11.80 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.20), residues: 1972 helix: 2.59 (0.14), residues: 1308 sheet: 1.01 (0.48), residues: 116 loop : 0.23 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 390 TYR 0.016 0.001 TYR B 531 PHE 0.007 0.001 PHE B 658 TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00313 (17280) covalent geometry : angle 0.53461 (23152) SS BOND : angle 0.00000 ( 8) hydrogen bonds : bond 0.03147 ( 1016) hydrogen bonds : angle 3.47446 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.04 seconds wall clock time: 56 minutes 11.74 seconds (3371.74 seconds total)