Starting phenix.real_space_refine on Sat Sep 28 00:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_0093.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_0093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_0093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_0093.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/09_2024/6gyn_0093.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 132 5.16 5 C 11148 2.51 5 N 2684 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C Time building chain proxies: 13.63, per 1000 atoms: 0.80 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 2.1 seconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 70.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 259 through 286 removed outlier: 3.759A pdb=" N PHE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 292 through 313 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP A 345 " --> pdb=" O TRP A 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.564A pdb=" N ARG A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 390 through 410 removed outlier: 3.792A pdb=" N ILE A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.527A pdb=" N GLN A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 488 through 518 removed outlier: 3.699A pdb=" N TRP A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 259 through 286 removed outlier: 3.758A pdb=" N PHE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Proline residue: B 281 - end of helix Processing helix chain 'B' and resid 292 through 313 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.893A pdb=" N LYS B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 350 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Proline residue: B 440 - end of helix removed outlier: 3.526A pdb=" N GLN B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 4.020A pdb=" N GLU B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 696 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 Processing helix chain 'C' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU C 222 " --> pdb=" O PHE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Proline residue: C 281 - end of helix Processing helix chain 'C' and resid 292 through 313 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP C 345 " --> pdb=" O TRP C 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Proline residue: C 440 - end of helix removed outlier: 3.525A pdb=" N GLN C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP C 493 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR C 559 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 573 Processing helix chain 'C' and resid 574 through 591 removed outlier: 5.580A pdb=" N LYS C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU C 589 " --> pdb=" O ASN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 Processing helix chain 'C' and resid 609 through 611 No H-bonds generated for 'chain 'C' and resid 609 through 611' Processing helix chain 'C' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 696 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 708 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Proline residue: D 281 - end of helix Processing helix chain 'D' and resid 292 through 313 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS D 339 " --> pdb=" O MET D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP D 345 " --> pdb=" O TRP D 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 350 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 410 " --> pdb=" O HIS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 443 removed outlier: 3.694A pdb=" N PHE D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Proline residue: D 440 - end of helix removed outlier: 3.525A pdb=" N GLN D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 460 through 475 Processing helix chain 'D' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP D 493 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR D 559 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 Processing helix chain 'D' and resid 574 through 591 removed outlier: 5.579A pdb=" N LYS D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU D 589 " --> pdb=" O ASN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 609 through 611 No H-bonds generated for 'chain 'D' and resid 609 through 611' Processing helix chain 'D' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 696 " --> pdb=" O VAL D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 616 removed outlier: 6.574A pdb=" N ARG A 680 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR A 621 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 675 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 612 through 616 removed outlier: 6.572A pdb=" N ARG B 680 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR B 621 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 675 " --> pdb=" O TYR B 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG C 680 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR C 621 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 675 " --> pdb=" O TYR C 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG D 680 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR D 621 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 675 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 4.85 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: 9870 14.30 - 28.61: 458 28.61 - 42.91: 116 42.91 - 57.21: 60 57.21 - 71.51: 16 Dihedral angle restraints: 10520 sinusoidal: 4692 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 10517 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: 0.00 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: 0.490 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 41.810 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- 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= 0.520 Angle : 0.849 7.511 23152 Z= 0.454 Chirality : 0.052 0.324 2492 Planarity : 0.006 0.052 2820 Dihedral : 10.497 71.515 6760 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 1972 helix: -1.78 (0.11), residues: 1312 sheet: 0.54 (0.48), residues: 116 loop : -1.46 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 401 HIS 0.010 0.002 HIS D 475 PHE 0.024 0.002 PHE B 379 TYR 0.032 0.003 TYR C 633 ARG 0.009 0.001 ARG B 396 *********************** 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 fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8756 (mmm) cc_final: 0.8070 (mpp) REVERT: A 331 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7481 (mm-40) REVERT: A 335 MET cc_start: 0.7963 (mmm) cc_final: 0.7503 (mmm) REVERT: A 407 MET cc_start: 0.8456 (tpp) cc_final: 0.8184 (tpt) REVERT: A 432 ASP cc_start: 0.8659 (t70) cc_final: 0.8380 (t70) REVERT: B 308 ILE cc_start: 0.8976 (mt) cc_final: 0.8775 (tt) REVERT: B 331 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 335 MET cc_start: 0.8080 (mmm) cc_final: 0.7591 (mmm) REVERT: B 407 MET cc_start: 0.8465 (tpp) cc_final: 0.8168 (tpt) REVERT: B 432 ASP cc_start: 0.8657 (t70) cc_final: 0.8363 (t70) REVERT: B 449 CYS cc_start: 0.8414 (p) cc_final: 0.8126 (p) REVERT: C 308 ILE cc_start: 0.8972 (mt) cc_final: 0.8770 (tt) REVERT: C 331 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7455 (mm-40) REVERT: C 335 MET cc_start: 0.8086 (mmm) cc_final: 0.7599 (mmm) REVERT: C 407 MET cc_start: 0.8464 (tpp) cc_final: 0.8166 (tpt) REVERT: C 432 ASP cc_start: 0.8655 (t70) cc_final: 0.8355 (t70) REVERT: C 449 CYS cc_start: 0.8407 (p) cc_final: 0.8113 (p) REVERT: D 308 ILE cc_start: 0.8974 (mt) cc_final: 0.8771 (tt) REVERT: D 331 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7454 (mm-40) REVERT: D 335 MET cc_start: 0.8087 (mmm) cc_final: 0.7599 (mmm) REVERT: D 407 MET cc_start: 0.8461 (tpp) cc_final: 0.8165 (tpt) REVERT: D 432 ASP cc_start: 0.8652 (t70) cc_final: 0.8355 (t70) REVERT: D 449 CYS cc_start: 0.8400 (p) cc_final: 0.8128 (p) REVERT: D 473 MET cc_start: 0.8524 (ttm) cc_final: 0.8233 (ttm) REVERT: D 593 MET cc_start: 0.8534 (ttt) cc_final: 0.8334 (ttt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2890 time to fit residues: 130.2440 Evaluate side-chains 162 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 541 HIS B 459 ASN B 541 HIS C 223 GLN C 459 ASN C 541 HIS D 223 GLN D 459 ASN D 541 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17280 Z= 0.283 Angle : 0.573 7.773 23152 Z= 0.294 Chirality : 0.043 0.123 2492 Planarity : 0.004 0.033 2820 Dihedral : 10.401 72.477 2960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 1972 helix: 0.45 (0.13), residues: 1340 sheet: 0.67 (0.48), residues: 116 loop : -0.89 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 401 HIS 0.005 0.002 HIS A 475 PHE 0.012 0.001 PHE B 689 TYR 0.016 0.002 TYR B 633 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 2.047 Fit side-chains REVERT: A 331 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7401 (mm-40) REVERT: A 335 MET cc_start: 0.8119 (mmm) cc_final: 0.7526 (mmm) REVERT: B 304 THR cc_start: 0.9415 (m) cc_final: 0.9209 (p) REVERT: B 331 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7397 (mm-40) REVERT: B 335 MET cc_start: 0.8084 (mmm) cc_final: 0.7433 (mmm) REVERT: C 304 THR cc_start: 0.9414 (m) cc_final: 0.9208 (p) REVERT: C 331 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7386 (mm-40) REVERT: C 335 MET cc_start: 0.8065 (mmm) cc_final: 0.7457 (mmm) REVERT: D 304 THR cc_start: 0.9414 (m) cc_final: 0.9210 (p) REVERT: D 331 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7382 (mm-40) REVERT: D 335 MET cc_start: 0.8068 (mmm) cc_final: 0.7458 (mmm) REVERT: D 473 MET cc_start: 0.8451 (ttm) cc_final: 0.8234 (ttm) outliers start: 20 outliers final: 9 residues processed: 210 average time/residue: 0.2557 time to fit residues: 85.5978 Evaluate side-chains 171 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 158 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS B 406 HIS B 475 HIS C 223 GLN C 406 HIS C 475 HIS D 223 GLN D 475 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17280 Z= 0.201 Angle : 0.506 5.858 23152 Z= 0.260 Chirality : 0.040 0.118 2492 Planarity : 0.003 0.032 2820 Dihedral : 10.004 68.287 2960 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1972 helix: 1.34 (0.14), residues: 1324 sheet: 0.53 (0.48), residues: 116 loop : -0.39 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 401 HIS 0.004 0.001 HIS A 475 PHE 0.013 0.001 PHE C 252 TYR 0.016 0.001 TYR B 531 ARG 0.002 0.000 ARG A 390 *********************** 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 210 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 2.075 Fit side-chains REVERT: A 331 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7627 (mm-40) REVERT: A 335 MET cc_start: 0.8263 (mmm) cc_final: 0.7809 (mmm) REVERT: B 303 ASP cc_start: 0.8192 (m-30) cc_final: 0.7977 (m-30) REVERT: B 304 THR cc_start: 0.9467 (m) cc_final: 0.9256 (p) REVERT: B 331 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 335 MET cc_start: 0.8241 (mmm) cc_final: 0.7777 (mmm) REVERT: B 449 CYS cc_start: 0.8152 (p) cc_final: 0.7656 (p) REVERT: C 303 ASP cc_start: 0.8195 (m-30) cc_final: 0.7978 (m-30) REVERT: C 304 THR cc_start: 0.9467 (m) cc_final: 0.9255 (p) REVERT: C 331 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7618 (mm-40) REVERT: C 335 MET cc_start: 0.8244 (mmm) cc_final: 0.7781 (mmm) REVERT: C 449 CYS cc_start: 0.8153 (p) cc_final: 0.7668 (p) REVERT: D 303 ASP cc_start: 0.8192 (m-30) cc_final: 0.7974 (m-30) REVERT: D 304 THR cc_start: 0.9467 (m) cc_final: 0.9256 (p) REVERT: D 331 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7614 (mm-40) REVERT: D 335 MET cc_start: 0.8246 (mmm) cc_final: 0.7786 (mmm) REVERT: D 449 CYS cc_start: 0.8171 (p) cc_final: 0.7684 (p) outliers start: 28 outliers final: 21 residues processed: 198 average time/residue: 0.2307 time to fit residues: 75.2229 Evaluate side-chains 180 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 398 ILE 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 176 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17280 Z= 0.149 Angle : 0.477 8.550 23152 Z= 0.241 Chirality : 0.040 0.115 2492 Planarity : 0.003 0.031 2820 Dihedral : 9.807 63.243 2960 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.99 % Allowed : 10.17 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1972 helix: 1.88 (0.14), residues: 1304 sheet: 0.51 (0.47), residues: 116 loop : -0.13 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 401 HIS 0.002 0.001 HIS D 406 PHE 0.011 0.001 PHE A 658 TYR 0.015 0.001 TYR B 531 ARG 0.002 0.000 ARG C 390 *********************** 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 197 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 2.115 Fit side-chains REVERT: A 331 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7286 (mm-40) REVERT: A 335 MET cc_start: 0.8249 (mmm) cc_final: 0.7556 (mmm) REVERT: A 449 CYS cc_start: 0.7834 (p) cc_final: 0.7364 (p) REVERT: A 538 MET cc_start: 0.8787 (mtm) cc_final: 0.8082 (mtm) REVERT: B 335 MET cc_start: 0.8226 (mmm) cc_final: 0.7776 (mmm) REVERT: B 449 CYS cc_start: 0.7865 (p) cc_final: 0.7424 (p) REVERT: B 494 LEU cc_start: 0.8884 (mt) cc_final: 0.8603 (mt) REVERT: B 538 MET cc_start: 0.8776 (mtm) cc_final: 0.8139 (mtm) REVERT: C 335 MET cc_start: 0.8226 (mmm) cc_final: 0.7779 (mmm) REVERT: C 449 CYS cc_start: 0.7903 (p) cc_final: 0.7462 (p) REVERT: C 538 MET cc_start: 0.8777 (mtm) cc_final: 0.8140 (mtm) REVERT: D 335 MET cc_start: 0.8225 (mmm) cc_final: 0.7780 (mmm) REVERT: D 449 CYS cc_start: 0.7818 (p) cc_final: 0.7366 (p) REVERT: D 538 MET cc_start: 0.8778 (mtm) cc_final: 0.8137 (mtm) REVERT: D 593 MET cc_start: 0.8072 (ttp) cc_final: 0.7860 (ttp) outliers start: 17 outliers final: 13 residues processed: 192 average time/residue: 0.2219 time to fit residues: 71.7002 Evaluate side-chains 172 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 170 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 459 ASN C 459 ASN D 406 HIS D 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17280 Z= 0.192 Angle : 0.496 8.946 23152 Z= 0.249 Chirality : 0.040 0.121 2492 Planarity : 0.003 0.029 2820 Dihedral : 9.700 58.325 2960 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.45 % Allowed : 9.59 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 1972 helix: 2.11 (0.14), residues: 1304 sheet: 0.54 (0.48), residues: 116 loop : -0.01 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 401 HIS 0.003 0.001 HIS D 406 PHE 0.008 0.001 PHE D 658 TYR 0.016 0.001 TYR B 531 ARG 0.001 0.000 ARG B 390 *********************** 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 192 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.745 Fit side-chains REVERT: A 331 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7219 (mm-40) REVERT: A 335 MET cc_start: 0.8178 (mmm) cc_final: 0.7528 (mmm) REVERT: A 424 MET cc_start: 0.8772 (tpp) cc_final: 0.8048 (tpp) REVERT: A 449 CYS cc_start: 0.7881 (p) cc_final: 0.7412 (p) REVERT: A 538 MET cc_start: 0.8863 (mtm) cc_final: 0.8569 (mtm) REVERT: A 593 MET cc_start: 0.8558 (ttp) cc_final: 0.7426 (ttp) REVERT: B 269 MET cc_start: 0.9134 (tpp) cc_final: 0.8911 (tpp) REVERT: B 331 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7131 (mm-40) REVERT: B 335 MET cc_start: 0.8167 (mmm) cc_final: 0.7532 (mmm) REVERT: B 424 MET cc_start: 0.8748 (tpp) cc_final: 0.8030 (tpp) REVERT: B 449 CYS cc_start: 0.7859 (p) cc_final: 0.7395 (p) REVERT: B 538 MET cc_start: 0.8870 (mtm) cc_final: 0.8391 (mtm) REVERT: B 593 MET cc_start: 0.8557 (ttp) cc_final: 0.7388 (ttp) REVERT: C 269 MET cc_start: 0.9137 (tpp) cc_final: 0.8911 (tpp) REVERT: C 331 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7125 (mm-40) REVERT: C 335 MET cc_start: 0.8166 (mmm) cc_final: 0.7533 (mmm) REVERT: C 449 CYS cc_start: 0.7895 (p) cc_final: 0.7425 (p) REVERT: C 538 MET cc_start: 0.8867 (mtm) cc_final: 0.8389 (mtm) REVERT: C 593 MET cc_start: 0.8551 (ttp) cc_final: 0.7385 (ttp) REVERT: D 269 MET cc_start: 0.9133 (tpp) cc_final: 0.8908 (tpp) REVERT: D 331 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7128 (mm-40) REVERT: D 335 MET cc_start: 0.8163 (mmm) cc_final: 0.7530 (mmm) REVERT: D 449 CYS cc_start: 0.7886 (p) cc_final: 0.7425 (p) REVERT: D 538 MET cc_start: 0.8870 (mtm) cc_final: 0.8390 (mtm) outliers start: 25 outliers final: 16 residues processed: 183 average time/residue: 0.2415 time to fit residues: 73.2013 Evaluate side-chains 173 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN C 475 HIS D 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17280 Z= 0.226 Angle : 0.508 9.199 23152 Z= 0.256 Chirality : 0.041 0.117 2492 Planarity : 0.003 0.028 2820 Dihedral : 9.579 54.255 2960 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.45 % Allowed : 9.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 1972 helix: 2.23 (0.14), residues: 1304 sheet: 0.66 (0.48), residues: 116 loop : 0.09 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 401 HIS 0.003 0.001 HIS D 256 PHE 0.007 0.001 PHE B 658 TYR 0.017 0.001 TYR A 531 ARG 0.002 0.000 ARG A 372 *********************** 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 186 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.915 Fit side-chains REVERT: A 331 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7235 (mm-40) REVERT: A 335 MET cc_start: 0.8169 (mmm) cc_final: 0.7545 (mmm) REVERT: A 424 MET cc_start: 0.8763 (tpp) cc_final: 0.8547 (tpp) REVERT: A 449 CYS cc_start: 0.7972 (p) cc_final: 0.7486 (p) REVERT: A 538 MET cc_start: 0.8865 (mtm) cc_final: 0.8294 (mtm) REVERT: A 593 MET cc_start: 0.8530 (ttp) cc_final: 0.7700 (ttp) REVERT: B 335 MET cc_start: 0.8149 (mmm) cc_final: 0.7526 (mmm) REVERT: B 449 CYS cc_start: 0.8028 (p) cc_final: 0.7563 (p) REVERT: B 538 MET cc_start: 0.8953 (mtm) cc_final: 0.8719 (mtm) REVERT: B 593 MET cc_start: 0.8510 (ttp) cc_final: 0.7633 (ttp) REVERT: C 335 MET cc_start: 0.8145 (mmm) cc_final: 0.7526 (mmm) REVERT: C 449 CYS cc_start: 0.8066 (p) cc_final: 0.7600 (p) REVERT: C 538 MET cc_start: 0.8909 (mtm) cc_final: 0.8670 (mtm) REVERT: C 593 MET cc_start: 0.8503 (ttp) cc_final: 0.7639 (ttp) REVERT: D 335 MET cc_start: 0.8145 (mmm) cc_final: 0.7525 (mmm) REVERT: D 449 CYS cc_start: 0.8064 (p) cc_final: 0.7602 (p) REVERT: D 538 MET cc_start: 0.8909 (mtm) cc_final: 0.8666 (mtm) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.2428 time to fit residues: 68.0838 Evaluate side-chains 172 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 297 VAL 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 252 PHE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 297 VAL 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 182 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN D 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17280 Z= 0.156 Angle : 0.477 9.328 23152 Z= 0.238 Chirality : 0.040 0.129 2492 Planarity : 0.003 0.029 2820 Dihedral : 9.131 55.333 2960 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.05 % Allowed : 10.23 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.20), residues: 1972 helix: 2.39 (0.14), residues: 1304 sheet: 0.84 (0.49), residues: 116 loop : 0.16 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 401 HIS 0.002 0.001 HIS B 399 PHE 0.009 0.001 PHE C 658 TYR 0.015 0.001 TYR B 531 ARG 0.001 0.000 ARG C 390 *********************** 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 196 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.907 Fit side-chains REVERT: A 331 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7216 (mm-40) REVERT: A 335 MET cc_start: 0.8135 (mmm) cc_final: 0.7531 (mmm) REVERT: A 424 MET cc_start: 0.8753 (tpp) cc_final: 0.8476 (tpp) REVERT: A 449 CYS cc_start: 0.7854 (p) cc_final: 0.7338 (p) REVERT: A 494 LEU cc_start: 0.8890 (mt) cc_final: 0.8600 (mt) REVERT: A 538 MET cc_start: 0.8935 (mtm) cc_final: 0.8572 (mtm) REVERT: A 593 MET cc_start: 0.8437 (ttp) cc_final: 0.7484 (ttp) REVERT: B 335 MET cc_start: 0.8134 (mmm) cc_final: 0.7729 (mmm) REVERT: B 449 CYS cc_start: 0.7818 (p) cc_final: 0.7309 (p) REVERT: B 494 LEU cc_start: 0.8878 (mt) cc_final: 0.8597 (mt) REVERT: B 593 MET cc_start: 0.8514 (ttp) cc_final: 0.7624 (ttp) REVERT: C 335 MET cc_start: 0.8130 (mmm) cc_final: 0.7728 (mmm) REVERT: C 449 CYS cc_start: 0.7849 (p) cc_final: 0.7351 (p) REVERT: C 494 LEU cc_start: 0.8892 (mt) cc_final: 0.8602 (mt) REVERT: C 593 MET cc_start: 0.8509 (ttp) cc_final: 0.7628 (ttp) REVERT: D 335 MET cc_start: 0.8129 (mmm) cc_final: 0.7730 (mmm) REVERT: D 449 CYS cc_start: 0.7857 (p) cc_final: 0.7349 (p) REVERT: D 494 LEU cc_start: 0.8876 (mt) cc_final: 0.8593 (mt) outliers start: 18 outliers final: 11 residues processed: 188 average time/residue: 0.2222 time to fit residues: 69.7520 Evaluate side-chains 176 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN D 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2648 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= 0.161 Angle : 0.488 9.082 23152 Z= 0.245 Chirality : 0.040 0.115 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.862 53.455 2960 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.22 % Allowed : 11.05 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1972 helix: 2.48 (0.14), residues: 1304 sheet: 0.91 (0.49), residues: 116 loop : 0.23 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 401 HIS 0.002 0.001 HIS B 406 PHE 0.007 0.001 PHE A 658 TYR 0.015 0.001 TYR A 531 ARG 0.001 0.000 ARG A 372 *********************** 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 189 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.997 Fit side-chains REVERT: A 331 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7206 (mm-40) REVERT: A 335 MET cc_start: 0.8139 (mmm) cc_final: 0.7494 (mmm) REVERT: A 424 MET cc_start: 0.8753 (tpp) cc_final: 0.8490 (tpp) REVERT: A 432 ASP cc_start: 0.8447 (t0) cc_final: 0.8233 (t0) REVERT: A 449 CYS cc_start: 0.7837 (p) cc_final: 0.7329 (p) REVERT: A 494 LEU cc_start: 0.8892 (mt) cc_final: 0.8601 (mt) REVERT: A 538 MET cc_start: 0.8889 (mtm) cc_final: 0.8623 (mtm) REVERT: A 593 MET cc_start: 0.8489 (ttp) cc_final: 0.7602 (ttp) REVERT: B 335 MET cc_start: 0.8123 (mmm) cc_final: 0.7706 (mmm) REVERT: B 424 MET cc_start: 0.8760 (tpp) cc_final: 0.7999 (tpp) REVERT: B 449 CYS cc_start: 0.7937 (p) cc_final: 0.7506 (p) REVERT: B 494 LEU cc_start: 0.8876 (mt) cc_final: 0.8588 (mt) REVERT: B 538 MET cc_start: 0.8778 (mtm) cc_final: 0.8176 (mtm) REVERT: B 593 MET cc_start: 0.8484 (ttp) cc_final: 0.7563 (ttp) REVERT: C 335 MET cc_start: 0.8125 (mmm) cc_final: 0.7747 (mmm) REVERT: C 424 MET cc_start: 0.8734 (tpp) cc_final: 0.8505 (tpp) REVERT: C 449 CYS cc_start: 0.7988 (p) cc_final: 0.7568 (p) REVERT: C 494 LEU cc_start: 0.8895 (mt) cc_final: 0.8603 (mt) REVERT: C 538 MET cc_start: 0.8781 (mtm) cc_final: 0.8185 (mtm) REVERT: C 593 MET cc_start: 0.8481 (ttp) cc_final: 0.7567 (ttp) REVERT: D 335 MET cc_start: 0.8116 (mmm) cc_final: 0.7699 (mmm) REVERT: D 424 MET cc_start: 0.8738 (tpp) cc_final: 0.8507 (tpp) REVERT: D 449 CYS cc_start: 0.7969 (p) cc_final: 0.7554 (p) REVERT: D 494 LEU cc_start: 0.8883 (mt) cc_final: 0.8600 (mt) REVERT: D 538 MET cc_start: 0.8781 (mtm) cc_final: 0.8177 (mtm) REVERT: D 593 MET cc_start: 0.8504 (ttp) cc_final: 0.7364 (ttp) outliers start: 21 outliers final: 13 residues processed: 178 average time/residue: 0.2252 time to fit residues: 66.3287 Evaluate side-chains 179 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 223 GLN D 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2711 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= 0.203 Angle : 0.521 10.736 23152 Z= 0.258 Chirality : 0.041 0.116 2492 Planarity : 0.003 0.028 2820 Dihedral : 8.908 53.847 2960 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.28 % Allowed : 11.10 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 1972 helix: 2.43 (0.14), residues: 1308 sheet: 0.93 (0.49), residues: 116 loop : 0.24 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 401 HIS 0.003 0.001 HIS B 406 PHE 0.007 0.001 PHE B 658 TYR 0.018 0.001 TYR D 531 ARG 0.002 0.000 ARG C 393 *********************** 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 182 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.893 Fit side-chains REVERT: A 214 MET cc_start: 0.6744 (mtt) cc_final: 0.6338 (tpp) REVERT: A 331 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7205 (mm-40) REVERT: A 335 MET cc_start: 0.8068 (mmm) cc_final: 0.7492 (mmm) REVERT: A 424 MET cc_start: 0.8749 (tpp) cc_final: 0.8490 (tpp) REVERT: A 432 ASP cc_start: 0.8430 (t0) cc_final: 0.8228 (t0) REVERT: A 449 CYS cc_start: 0.7910 (p) cc_final: 0.7411 (p) REVERT: A 538 MET cc_start: 0.8913 (mtm) cc_final: 0.8699 (mtm) REVERT: A 563 MET cc_start: 0.8594 (tpp) cc_final: 0.8292 (tpt) REVERT: A 593 MET cc_start: 0.8514 (ttp) cc_final: 0.7631 (ttp) REVERT: B 303 ASP cc_start: 0.8103 (m-30) cc_final: 0.7640 (t0) REVERT: B 335 MET cc_start: 0.8040 (mmm) cc_final: 0.7669 (mmm) REVERT: B 424 MET cc_start: 0.8798 (tpp) cc_final: 0.8001 (tpp) REVERT: B 432 ASP cc_start: 0.8447 (t0) cc_final: 0.8238 (t0) REVERT: B 449 CYS cc_start: 0.8016 (p) cc_final: 0.7590 (p) REVERT: B 494 LEU cc_start: 0.8921 (mt) cc_final: 0.8629 (mt) REVERT: B 538 MET cc_start: 0.8808 (mtm) cc_final: 0.8208 (mtm) REVERT: B 593 MET cc_start: 0.8511 (ttp) cc_final: 0.7591 (ttp) REVERT: C 303 ASP cc_start: 0.8102 (m-30) cc_final: 0.7639 (t0) REVERT: C 335 MET cc_start: 0.8033 (mmm) cc_final: 0.7667 (mmm) REVERT: C 432 ASP cc_start: 0.8397 (t0) cc_final: 0.8187 (t0) REVERT: C 449 CYS cc_start: 0.8043 (p) cc_final: 0.7628 (p) REVERT: C 494 LEU cc_start: 0.8927 (mt) cc_final: 0.8623 (mt) REVERT: C 538 MET cc_start: 0.8811 (mtm) cc_final: 0.8214 (mtm) REVERT: C 593 MET cc_start: 0.8506 (ttp) cc_final: 0.7598 (ttp) REVERT: D 335 MET cc_start: 0.8039 (mmm) cc_final: 0.7669 (mmm) REVERT: D 432 ASP cc_start: 0.8394 (t0) cc_final: 0.8190 (t0) REVERT: D 449 CYS cc_start: 0.8028 (p) cc_final: 0.7608 (p) REVERT: D 494 LEU cc_start: 0.8925 (mt) cc_final: 0.8635 (mt) REVERT: D 538 MET cc_start: 0.8811 (mtm) cc_final: 0.8204 (mtm) REVERT: D 563 MET cc_start: 0.8598 (tpp) cc_final: 0.8302 (tpt) REVERT: D 593 MET cc_start: 0.8486 (ttp) cc_final: 0.7083 (ttp) outliers start: 22 outliers final: 13 residues processed: 172 average time/residue: 0.2285 time to fit residues: 65.1650 Evaluate side-chains 173 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 473 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17280 Z= 0.131 Angle : 0.498 9.847 23152 Z= 0.245 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.656 53.409 2960 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.64 % Allowed : 11.80 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.20), residues: 1972 helix: 2.55 (0.14), residues: 1304 sheet: 1.01 (0.49), residues: 116 loop : 0.29 (0.30), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.000 HIS D 406 PHE 0.006 0.001 PHE B 658 TYR 0.016 0.001 TYR C 531 ARG 0.001 0.000 ARG A 578 ********************** 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 fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 1.941 Fit side-chains REVERT: A 335 MET cc_start: 0.8012 (mmm) cc_final: 0.7377 (mmm) REVERT: A 424 MET cc_start: 0.8752 (tpp) cc_final: 0.8478 (tpp) REVERT: A 449 CYS cc_start: 0.7896 (p) cc_final: 0.7467 (p) REVERT: A 494 LEU cc_start: 0.8823 (mt) cc_final: 0.8518 (mt) REVERT: A 538 MET cc_start: 0.8870 (mtm) cc_final: 0.8628 (mtm) REVERT: A 593 MET cc_start: 0.8463 (ttp) cc_final: 0.7589 (ttp) REVERT: B 335 MET cc_start: 0.7863 (mmm) cc_final: 0.7296 (mmm) REVERT: B 424 MET cc_start: 0.8763 (tpp) cc_final: 0.7946 (tpp) REVERT: B 432 ASP cc_start: 0.8405 (t0) cc_final: 0.8195 (t0) REVERT: B 449 CYS cc_start: 0.7874 (p) cc_final: 0.7446 (p) REVERT: B 494 LEU cc_start: 0.8819 (mt) cc_final: 0.8522 (mt) REVERT: B 538 MET cc_start: 0.8764 (mtm) cc_final: 0.8144 (mtm) REVERT: B 593 MET cc_start: 0.8443 (ttp) cc_final: 0.7529 (ttp) REVERT: C 335 MET cc_start: 0.7854 (mmm) cc_final: 0.7291 (mmm) REVERT: C 424 MET cc_start: 0.8723 (tpp) cc_final: 0.7883 (tpp) REVERT: C 432 ASP cc_start: 0.8403 (t0) cc_final: 0.8195 (t0) REVERT: C 449 CYS cc_start: 0.7890 (p) cc_final: 0.7475 (p) REVERT: C 538 MET cc_start: 0.8766 (mtm) cc_final: 0.8150 (mtm) REVERT: C 593 MET cc_start: 0.8437 (ttp) cc_final: 0.7533 (ttp) REVERT: D 335 MET cc_start: 0.7860 (mmm) cc_final: 0.7292 (mmm) REVERT: D 432 ASP cc_start: 0.8401 (t0) cc_final: 0.8187 (t0) REVERT: D 449 CYS cc_start: 0.7891 (p) cc_final: 0.7470 (p) REVERT: D 494 LEU cc_start: 0.8807 (mt) cc_final: 0.8508 (mt) REVERT: D 538 MET cc_start: 0.8758 (mtm) cc_final: 0.8138 (mtm) REVERT: D 593 MET cc_start: 0.8435 (ttp) cc_final: 0.6981 (ttp) outliers start: 11 outliers final: 10 residues processed: 195 average time/residue: 0.2261 time to fit residues: 73.2453 Evaluate side-chains 179 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083366 restraints weight = 30756.701| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.42 r_work: 0.2940 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17280 Z= 0.208 Angle : 0.538 9.789 23152 Z= 0.261 Chirality : 0.041 0.150 2492 Planarity : 0.003 0.028 2820 Dihedral : 8.788 53.793 2960 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.87 % Allowed : 12.15 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.20), residues: 1972 helix: 2.50 (0.14), residues: 1312 sheet: 0.96 (0.49), residues: 116 loop : 0.27 (0.30), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS C 256 PHE 0.007 0.001 PHE D 658 TYR 0.018 0.001 TYR B 531 ARG 0.002 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.13 seconds wall clock time: 54 minutes 34.70 seconds (3274.70 seconds total)