Starting phenix.real_space_refine on Mon Oct 14 19:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpf_16151/10_2024/8bpf_16151.cif" } resolution = 3.5 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= 0.001 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 11697 2.51 5 N 3148 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18593 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1790 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1756 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "C" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain breaks: 1 Chain: "K" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1778 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "L" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 115} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.05, per 1000 atoms: 0.70 Number of scatterers: 18593 At special positions: 0 Unit cell: (189, 100.44, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 3654 8.00 N 3148 7.00 C 11697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 414 " - pdb=" SG CYS C 414 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.04 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 58 " distance=1.58 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " " NAG M 1 " - " ASN J 48 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.3 seconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 58 sheets defined 12.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.792A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.610A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.689A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.855A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.650A pdb=" N ASN B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.576A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.908A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 removed outlier: 4.248A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 531 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.821A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N GLY E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 466 removed outlier: 3.710A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'E' and resid 553 through 557 removed outlier: 3.553A pdb=" N THR E 556 " --> pdb=" O ASP E 553 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY E 557 " --> pdb=" O LYS E 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 553 through 557' Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.687A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 4.001A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 466 removed outlier: 3.545A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'F' and resid 553 through 558 removed outlier: 3.562A pdb=" N GLY F 557 " --> pdb=" O LYS F 554 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS F 558 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.958A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 525 through 529 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 524 through 529 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 116 through 120 Processing helix chain 'K' and resid 353 through 360 removed outlier: 3.538A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.807A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 removed outlier: 3.536A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 500 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'L' and resid 526 through 530 removed outlier: 3.947A pdb=" N ASN L 529 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 384 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.142A pdb=" N THR A 477 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 517 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.688A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.688A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 534 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 7.201A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 569 Processing sheet with id=AA9, first strand: chain 'B' and resid 379 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.821A pdb=" N TYR B 534 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 552 " --> pdb=" O TYR B 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 350 removed outlier: 4.292A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.611A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 428 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 437 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS C 430 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 435 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 520 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 476 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.566A pdb=" N MET C 489 " --> pdb=" O THR C 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.972A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 365 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 379 through 383 removed outlier: 4.253A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.529A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.529A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC5, first strand: chain 'D' and resid 565 through 567 removed outlier: 3.683A pdb=" N LEU D 566 " --> pdb=" O SER E 565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL E 567 " --> pdb=" O LEU D 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.591A pdb=" N ILE E 350 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 368 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY E 409 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU E 372 " --> pdb=" O PHE E 405 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD1, first strand: chain 'F' and resid 346 through 350 removed outlier: 4.093A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 370 " --> pdb=" O ARG F 346 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 380 through 383 removed outlier: 4.061A pdb=" N PHE F 424 " --> pdb=" O ILE F 441 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 441 " --> pdb=" O PHE F 424 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.825A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.825A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 566 through 567 Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.749A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 379 through 381 Processing sheet with id=AD9, first strand: chain 'G' and resid 399 through 400 removed outlier: 3.742A pdb=" N THR G 404 " --> pdb=" O HIS G 400 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.619A pdb=" N THR G 473 " --> pdb=" O LEU G 457 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 469 through 471 Processing sheet with id=AE3, first strand: chain 'G' and resid 485 through 489 Processing sheet with id=AE4, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.534A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU H 372 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.351A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.654A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 501 " --> pdb=" O ILE H 520 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.654A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'H' and resid 562 through 564 removed outlier: 6.214A pdb=" N ASN H 563 " --> pdb=" O VAL K 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.681A pdb=" N CYS I 37 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.590A pdb=" N CYS I 104 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN I 116 " --> pdb=" O CYS I 104 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.806A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF5, first strand: chain 'J' and resid 103 through 104 removed outlier: 6.677A pdb=" N TYR J 103 " --> pdb=" O CYS L 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AF7, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.377A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.574A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR K 425 " --> pdb=" O THR K 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.524A pdb=" N TYR K 455 " --> pdb=" O LEU K 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 487 through 489 removed outlier: 3.583A pdb=" N MET K 489 " --> pdb=" O THR K 535 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR K 535 " --> pdb=" O MET K 489 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 454 through 457 removed outlier: 3.923A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AG4, first strand: chain 'L' and resid 489 through 490 557 hydrogen bonds defined for protein. 1383 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: 5.66 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5614 1.34 - 1.46: 4144 1.46 - 1.58: 9163 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 19049 Sorted by residual: bond pdb=" C MET B 568 " pdb=" N SER B 569 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.33e-02 5.65e+03 1.34e+01 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL L 552 " pdb=" CA VAL L 552 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL C 390 " pdb=" CA VAL C 390 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" N VAL A 538 " pdb=" CA VAL A 538 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.11e+01 ... (remaining 19044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 24012 1.59 - 3.19: 1798 3.19 - 4.78: 226 4.78 - 6.37: 21 6.37 - 7.97: 5 Bond angle restraints: 26062 Sorted by residual: angle pdb=" CA ARG L 546 " pdb=" CB ARG L 546 " pdb=" CG ARG L 546 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 angle pdb=" N LEU C 466 " pdb=" CA LEU C 466 " pdb=" C LEU C 466 " ideal model delta sigma weight residual 114.62 110.14 4.48 1.14e+00 7.69e-01 1.55e+01 angle pdb=" N ASN A 545 " pdb=" CA ASN A 545 " pdb=" C ASN A 545 " ideal model delta sigma weight residual 113.16 108.32 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" CA ALA F 482 " pdb=" C ALA F 482 " pdb=" O ALA F 482 " ideal model delta sigma weight residual 122.37 117.94 4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" CA ASP I 111 " pdb=" C ASP I 111 " pdb=" O ASP I 111 " ideal model delta sigma weight residual 121.36 116.82 4.54 1.20e+00 6.94e-01 1.43e+01 ... (remaining 26057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10719 17.97 - 35.94: 844 35.94 - 53.91: 147 53.91 - 71.88: 27 71.88 - 89.85: 20 Dihedral angle restraints: 11757 sinusoidal: 4793 harmonic: 6964 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual -86.00 -173.30 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS J 14 " pdb=" SG CYS J 14 " pdb=" SG CYS L 575 " pdb=" CB CYS L 575 " ideal model delta sinusoidal sigma weight residual 93.00 174.02 -81.02 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual 93.00 156.85 -63.85 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 11754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 3041 0.162 - 0.325: 50 0.325 - 0.487: 3 0.487 - 0.650: 0 0.650 - 0.812: 1 Chirality restraints: 3095 Sorted by residual: chirality pdb=" C1 NAG F 601 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG F 601 " pdb=" O5 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 563 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 3092 not shown) Planarity restraints: 3338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 563 " -0.054 2.00e-02 2.50e+03 6.90e-02 5.95e+01 pdb=" CG ASN A 563 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 563 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 563 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 563 " 0.041 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN E 563 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 563 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 563 " -0.073 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.042 2.00e-02 2.50e+03 4.48e-02 2.50e+01 pdb=" CG ASN K 563 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.054 2.00e-02 2.50e+03 ... (remaining 3335 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4069 2.79 - 3.32: 17185 3.32 - 3.85: 28108 3.85 - 4.37: 31808 4.37 - 4.90: 55395 Nonbonded interactions: 136565 Sorted by model distance: nonbonded pdb=" OD1 ASN D 402 " pdb=" OG1 THR D 404 " model vdw 2.267 3.040 nonbonded pdb=" O LEU H 372 " pdb=" OG1 THR H 404 " model vdw 2.283 3.040 nonbonded pdb=" OG SER L 469 " pdb=" O VAL L 523 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR K 379 " pdb=" OG1 THR K 429 " model vdw 2.304 3.040 nonbonded pdb=" O ILE J 5 " pdb=" OG1 THR J 18 " model vdw 2.309 3.040 ... (remaining 136560 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 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'B' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'C' and (resid 346 through 568 or resid 601)) selection = (chain 'D' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'E' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'F' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'G' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) selection = (chain 'K' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.920 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.006 0.049 19049 Z= 0.409 Angle : 0.850 7.967 26062 Z= 0.555 Chirality : 0.062 0.812 3095 Planarity : 0.006 0.124 3327 Dihedral : 13.399 89.850 7134 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.72 (0.17), residues: 2344 helix: -1.45 (0.32), residues: 221 sheet: 0.04 (0.18), residues: 842 loop : -1.98 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 418 HIS 0.007 0.001 HIS A 450 PHE 0.028 0.002 PHE F 354 TYR 0.020 0.001 TYR F 500 ARG 0.005 0.000 ARG L 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8486 (pttt) cc_final: 0.7472 (mmtt) REVERT: A 445 LYS cc_start: 0.8064 (mttt) cc_final: 0.7862 (mtmm) REVERT: A 466 LEU cc_start: 0.8594 (mp) cc_final: 0.8347 (mm) REVERT: B 376 ASP cc_start: 0.8158 (p0) cc_final: 0.7834 (p0) REVERT: H 391 LYS cc_start: 0.8123 (tptt) cc_final: 0.7657 (tmtt) REVERT: I 121 ASN cc_start: 0.8569 (m110) cc_final: 0.8061 (m110) REVERT: J 22 ILE cc_start: 0.8427 (pt) cc_final: 0.8064 (pt) REVERT: J 31 ASP cc_start: 0.8731 (m-30) cc_final: 0.8482 (m-30) REVERT: K 506 MET cc_start: 0.7214 (mtt) cc_final: 0.7005 (mtt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.4567 time to fit residues: 219.4244 Evaluate side-chains 198 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 0.0770 chunk 135 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN H 395 ASN H 490 GLN J 45 ASN ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 HIS K 439 GLN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19049 Z= 0.218 Angle : 0.676 8.904 26062 Z= 0.352 Chirality : 0.048 0.204 3095 Planarity : 0.005 0.054 3327 Dihedral : 4.533 30.413 2801 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.68 % Rotamer: Outliers : 1.47 % Allowed : 10.26 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.45 (0.17), residues: 2344 helix: -1.45 (0.30), residues: 234 sheet: 0.36 (0.18), residues: 826 loop : -1.83 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 418 HIS 0.007 0.001 HIS B 430 PHE 0.029 0.002 PHE L 479 TYR 0.028 0.001 TYR H 562 ARG 0.008 0.001 ARG H 491 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8331 (pttt) cc_final: 0.7340 (mmtt) REVERT: A 423 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7272 (tmm160) REVERT: A 445 LYS cc_start: 0.8117 (mttt) cc_final: 0.7911 (mtmm) REVERT: B 376 ASP cc_start: 0.8128 (p0) cc_final: 0.7785 (p0) REVERT: C 373 THR cc_start: 0.6301 (t) cc_final: 0.4815 (p) REVERT: G 375 TYR cc_start: 0.7939 (m-10) cc_final: 0.7634 (m-80) REVERT: G 376 ASP cc_start: 0.6748 (p0) cc_final: 0.6221 (p0) REVERT: I 121 ASN cc_start: 0.8527 (m110) cc_final: 0.8032 (t0) REVERT: J 31 ASP cc_start: 0.8777 (m-30) cc_final: 0.8464 (m-30) REVERT: K 364 LYS cc_start: 0.7749 (ptpp) cc_final: 0.5676 (ptpp) REVERT: L 515 TYR cc_start: 0.7063 (m-80) cc_final: 0.6694 (m-80) REVERT: L 534 TYR cc_start: 0.8333 (m-10) cc_final: 0.7935 (m-10) outliers start: 31 outliers final: 17 residues processed: 239 average time/residue: 0.3616 time to fit residues: 124.5021 Evaluate side-chains 196 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 467 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS F 490 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19049 Z= 0.244 Angle : 0.655 11.494 26062 Z= 0.337 Chirality : 0.047 0.167 3095 Planarity : 0.005 0.050 3327 Dihedral : 4.458 27.908 2801 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.70 % Favored : 91.21 % Rotamer: Outliers : 1.84 % Allowed : 14.05 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.39 (0.17), residues: 2344 helix: -1.26 (0.31), residues: 236 sheet: 0.37 (0.18), residues: 832 loop : -1.81 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 528 HIS 0.007 0.001 HIS K 400 PHE 0.022 0.002 PHE L 479 TYR 0.019 0.001 TYR K 375 ARG 0.008 0.001 ARG H 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8434 (pttt) cc_final: 0.7689 (mmmt) REVERT: A 445 LYS cc_start: 0.8032 (mttt) cc_final: 0.7817 (mtmm) REVERT: B 376 ASP cc_start: 0.8098 (p0) cc_final: 0.7749 (p0) REVERT: G 375 TYR cc_start: 0.7883 (m-10) cc_final: 0.7533 (m-80) REVERT: G 376 ASP cc_start: 0.6973 (p0) cc_final: 0.6488 (p0) REVERT: H 391 LYS cc_start: 0.7398 (tptp) cc_final: 0.7177 (tptp) REVERT: J 31 ASP cc_start: 0.8745 (m-30) cc_final: 0.8446 (m-30) REVERT: L 515 TYR cc_start: 0.7443 (m-80) cc_final: 0.6853 (m-80) REVERT: L 534 TYR cc_start: 0.8560 (m-10) cc_final: 0.8163 (m-10) outliers start: 39 outliers final: 23 residues processed: 217 average time/residue: 0.3792 time to fit residues: 120.4303 Evaluate side-chains 200 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 405 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 467 ARG Chi-restraints excluded: chain L residue 451 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 109 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 110 optimal weight: 0.0070 chunk 200 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN H 395 ASN H 400 HIS H 490 GLN I 85 ASN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19049 Z= 0.235 Angle : 0.635 9.562 26062 Z= 0.326 Chirality : 0.046 0.153 3095 Planarity : 0.004 0.047 3327 Dihedral : 4.432 26.637 2801 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.32 % Favored : 91.60 % Rotamer: Outliers : 2.37 % Allowed : 16.37 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.34 (0.17), residues: 2344 helix: -1.24 (0.31), residues: 237 sheet: 0.40 (0.18), residues: 832 loop : -1.78 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 528 HIS 0.008 0.001 HIS K 400 PHE 0.022 0.002 PHE L 479 TYR 0.012 0.001 TYR C 562 ARG 0.010 0.000 ARG H 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8458 (pttt) cc_final: 0.7687 (mmmt) REVERT: A 445 LYS cc_start: 0.8026 (mttt) cc_final: 0.7817 (mtmm) REVERT: B 376 ASP cc_start: 0.8112 (p0) cc_final: 0.7771 (p0) REVERT: F 568 MET cc_start: 0.5920 (tpp) cc_final: 0.5078 (tpt) REVERT: G 375 TYR cc_start: 0.8029 (m-10) cc_final: 0.7625 (m-10) REVERT: G 376 ASP cc_start: 0.6973 (p0) cc_final: 0.6502 (p0) REVERT: H 391 LYS cc_start: 0.7447 (tptp) cc_final: 0.7121 (tptp) REVERT: J 31 ASP cc_start: 0.8753 (m-30) cc_final: 0.8495 (m-30) REVERT: K 467 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7421 (tpt90) REVERT: L 515 TYR cc_start: 0.7419 (m-80) cc_final: 0.6953 (m-10) REVERT: L 534 TYR cc_start: 0.8547 (m-10) cc_final: 0.8085 (m-10) outliers start: 50 outliers final: 30 residues processed: 220 average time/residue: 0.3646 time to fit residues: 116.1245 Evaluate side-chains 201 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 467 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 166 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 0.0270 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 201 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19049 Z= 0.173 Angle : 0.617 9.106 26062 Z= 0.313 Chirality : 0.045 0.153 3095 Planarity : 0.004 0.043 3327 Dihedral : 4.257 24.263 2801 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.81 % Favored : 92.11 % Rotamer: Outliers : 2.13 % Allowed : 17.36 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.26 (0.17), residues: 2344 helix: -1.21 (0.31), residues: 237 sheet: 0.48 (0.18), residues: 848 loop : -1.77 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 528 HIS 0.016 0.001 HIS G 400 PHE 0.021 0.001 PHE L 479 TYR 0.015 0.001 TYR F 375 ARG 0.005 0.000 ARG E 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8364 (pttt) cc_final: 0.7618 (mmmt) REVERT: B 376 ASP cc_start: 0.8098 (p0) cc_final: 0.7758 (p0) REVERT: G 375 TYR cc_start: 0.7991 (m-10) cc_final: 0.7538 (m-10) REVERT: G 376 ASP cc_start: 0.6906 (p0) cc_final: 0.6440 (p0) REVERT: H 441 ILE cc_start: 0.3359 (pt) cc_final: 0.2998 (tp) REVERT: J 31 ASP cc_start: 0.8774 (m-30) cc_final: 0.8525 (m-30) REVERT: K 364 LYS cc_start: 0.7648 (ptpp) cc_final: 0.7418 (mtmt) REVERT: L 515 TYR cc_start: 0.7455 (m-80) cc_final: 0.6915 (m-10) outliers start: 45 outliers final: 31 residues processed: 208 average time/residue: 0.3449 time to fit residues: 106.5855 Evaluate side-chains 194 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 0.0060 chunk 131 optimal weight: 0.6980 chunk 55 optimal weight: 0.0060 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19049 Z= 0.172 Angle : 0.623 15.517 26062 Z= 0.312 Chirality : 0.045 0.149 3095 Planarity : 0.004 0.052 3327 Dihedral : 4.141 22.259 2801 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.76 % Favored : 92.11 % Rotamer: Outliers : 2.41 % Allowed : 17.93 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % 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: -1.20 (0.17), residues: 2344 helix: -1.08 (0.31), residues: 235 sheet: 0.50 (0.18), residues: 850 loop : -1.72 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 528 HIS 0.010 0.001 HIS K 400 PHE 0.021 0.001 PHE L 479 TYR 0.016 0.001 TYR F 375 ARG 0.012 0.000 ARG H 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.8346 (pttt) cc_final: 0.7612 (mmmt) REVERT: B 376 ASP cc_start: 0.8076 (p0) cc_final: 0.7734 (p0) REVERT: G 375 TYR cc_start: 0.8022 (m-10) cc_final: 0.7567 (m-10) REVERT: G 376 ASP cc_start: 0.6904 (p0) cc_final: 0.6439 (p0) REVERT: G 385 GLN cc_start: 0.5311 (mm-40) cc_final: 0.4931 (mm-40) REVERT: H 441 ILE cc_start: 0.3207 (pt) cc_final: 0.2852 (tp) REVERT: I 121 ASN cc_start: 0.8704 (m110) cc_final: 0.7962 (t0) REVERT: J 31 ASP cc_start: 0.8761 (m-30) cc_final: 0.8495 (m-30) REVERT: K 558 LYS cc_start: 0.6132 (mppt) cc_final: 0.5931 (mppt) REVERT: L 515 TYR cc_start: 0.7490 (m-80) cc_final: 0.6929 (m-10) outliers start: 51 outliers final: 37 residues processed: 210 average time/residue: 0.3420 time to fit residues: 106.9200 Evaluate side-chains 200 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: