Starting phenix.real_space_refine on Mon Jun 16 12:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_16151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_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/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_16151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_16151.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_16151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpf_16151/06_2025/8bpf_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.46, per 1000 atoms: 0.72 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: 4.58 Conformation dependent library (CDL) restraints added in 2.4 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: 2.86 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: 6.37 Time building geometry restraints manager: 5.46 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: 6.740 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: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 46.300 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.530 ------------------------------------------------------------------------------- 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 : 0.007 0.453 19090 Z= 0.468 Angle : 0.900 22.834 26156 Z= 0.567 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01810 ( 11) link_NAG-ASN : angle 6.36976 ( 33) link_BETA1-4 : bond 0.02201 ( 1) link_BETA1-4 : angle 4.43257 ( 3) hydrogen bonds : bond 0.27200 ( 482) hydrogen bonds : angle 9.38645 ( 1383) SS BOND : bond 0.08429 ( 29) SS BOND : angle 4.05289 ( 58) covalent geometry : bond 0.00625 (19049) covalent geometry : angle 0.85044 (26062) *********************** 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 to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 2.379 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: 0.4266 time to fit residues: 205.4517 Evaluate side-chains 198 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.094914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063662 restraints weight = 65934.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.065811 restraints weight = 36012.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067082 restraints weight = 25679.367| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19090 Z= 0.151 Angle : 0.682 9.028 26156 Z= 0.355 Chirality : 0.048 0.201 3095 Planarity : 0.005 0.055 3327 Dihedral : 4.514 31.415 2801 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.53 % Favored : 91.42 % Rotamer: Outliers : 1.32 % Allowed : 10.41 % 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: -1.46 (0.17), residues: 2344 helix: -1.42 (0.30), residues: 235 sheet: 0.30 (0.18), residues: 837 loop : -1.83 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 418 HIS 0.008 0.001 HIS B 430 PHE 0.028 0.002 PHE L 479 TYR 0.026 0.001 TYR H 562 ARG 0.009 0.001 ARG H 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 11) link_NAG-ASN : angle 2.31202 ( 33) link_BETA1-4 : bond 0.00099 ( 1) link_BETA1-4 : angle 2.11358 ( 3) hydrogen bonds : bond 0.04871 ( 482) hydrogen bonds : angle 6.70999 ( 1383) SS BOND : bond 0.00529 ( 29) SS BOND : angle 1.26305 ( 58) covalent geometry : bond 0.00351 (19049) covalent geometry : angle 0.67572 (26062) *********************** 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 247 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 2.322 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: 0.8200 (pttt) cc_final: 0.7229 (mmtt) REVERT: A 423 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7217 (tmm160) REVERT: A 445 LYS cc_start: 0.8351 (mttt) cc_final: 0.8029 (mtmm) REVERT: B 376 ASP cc_start: 0.8479 (p0) cc_final: 0.8125 (p0) REVERT: C 373 THR cc_start: 0.6997 (t) cc_final: 0.5908 (p) REVERT: G 375 TYR cc_start: 0.8109 (m-10) cc_final: 0.7797 (m-80) REVERT: G 376 ASP cc_start: 0.7070 (p0) cc_final: 0.6591 (p0) REVERT: G 553 ASP cc_start: 0.7755 (t0) cc_final: 0.7465 (t70) REVERT: H 391 LYS cc_start: 0.8139 (tptt) cc_final: 0.7926 (tptp) REVERT: J 31 ASP cc_start: 0.8799 (m-30) cc_final: 0.8487 (m-30) REVERT: J 134 TYR cc_start: 0.6886 (m-80) cc_final: 0.6662 (m-10) REVERT: K 364 LYS cc_start: 0.7605 (ptpp) cc_final: 0.5883 (ptpp) REVERT: K 506 MET cc_start: 0.7831 (mtt) cc_final: 0.7494 (mtt) REVERT: L 515 TYR cc_start: 0.7298 (m-80) cc_final: 0.6948 (m-80) REVERT: L 534 TYR cc_start: 0.8418 (m-10) cc_final: 0.7996 (m-10) outliers start: 28 outliers final: 17 residues processed: 234 average time/residue: 0.3646 time to fit residues: 122.7643 Evaluate side-chains 194 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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 176 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 189 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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** ** B 545 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** H 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN I 85 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.091269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059666 restraints weight = 66544.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.061657 restraints weight = 37127.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.062795 restraints weight = 26934.469| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19090 Z= 0.242 Angle : 0.722 10.971 26156 Z= 0.373 Chirality : 0.049 0.178 3095 Planarity : 0.005 0.053 3327 Dihedral : 4.821 31.567 2801 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.36 % Rotamer: Outliers : 2.13 % Allowed : 14.24 % Favored : 83.63 % 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: -1.61 (0.17), residues: 2344 helix: -1.44 (0.30), residues: 242 sheet: 0.19 (0.18), residues: 829 loop : -1.93 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 488 HIS 0.007 0.002 HIS D 518 PHE 0.030 0.002 PHE D 479 TYR 0.018 0.002 TYR K 375 ARG 0.010 0.001 ARG L 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 11) link_NAG-ASN : angle 2.06991 ( 33) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 1.90990 ( 3) hydrogen bonds : bond 0.04705 ( 482) hydrogen bonds : angle 6.28429 ( 1383) SS BOND : bond 0.00638 ( 29) SS BOND : angle 1.48344 ( 58) covalent geometry : bond 0.00573 (19049) covalent geometry : angle 0.71537 (26062) *********************** 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 236 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 2.132 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: 0.8395 (pttt) cc_final: 0.7686 (mmmt) REVERT: A 445 LYS cc_start: 0.8232 (mttt) cc_final: 0.7914 (mtmm) REVERT: B 358 PHE cc_start: 0.8997 (t80) cc_final: 0.8582 (t80) REVERT: B 376 ASP cc_start: 0.8508 (p0) cc_final: 0.8162 (p0) REVERT: C 348 PHE cc_start: 0.8589 (m-80) cc_final: 0.8371 (m-80) REVERT: G 375 TYR cc_start: 0.8157 (m-10) cc_final: 0.7716 (m-10) REVERT: G 376 ASP cc_start: 0.7393 (p0) cc_final: 0.6956 (p0) REVERT: H 391 LYS cc_start: 0.8208 (tptt) cc_final: 0.7977 (tptp) REVERT: H 568 MET cc_start: 0.7405 (mtt) cc_final: 0.6738 (tmm) REVERT: I 71 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7827 (tm-30) REVERT: J 31 ASP cc_start: 0.8780 (m-30) cc_final: 0.8525 (m-30) REVERT: L 515 TYR cc_start: 0.7668 (m-80) cc_final: 0.7081 (m-80) REVERT: L 534 TYR cc_start: 0.8775 (m-10) cc_final: 0.8343 (m-10) outliers start: 45 outliers final: 27 residues processed: 217 average time/residue: 0.3490 time to fit residues: 111.0645 Evaluate side-chains 201 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER 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 C residue 506 MET 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 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 I residue 62 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 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 520 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 222 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 5 optimal weight: 0.0570 chunk 199 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 215 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN F 490 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.092244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060997 restraints weight = 66302.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064086 restraints weight = 42577.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064291 restraints weight = 26628.649| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19090 Z= 0.132 Angle : 0.638 9.709 26156 Z= 0.326 Chirality : 0.046 0.185 3095 Planarity : 0.005 0.048 3327 Dihedral : 4.538 28.526 2801 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.15 % Favored : 91.77 % Rotamer: Outliers : 2.27 % Allowed : 16.79 % Favored : 80.94 % 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: -1.48 (0.17), residues: 2344 helix: -1.42 (0.30), residues: 243 sheet: 0.27 (0.18), residues: 838 loop : -1.83 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 528 HIS 0.012 0.001 HIS F 430 PHE 0.022 0.001 PHE L 479 TYR 0.013 0.001 TYR E 375 ARG 0.009 0.000 ARG L 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 11) link_NAG-ASN : angle 1.57106 ( 33) link_BETA1-4 : bond 0.00593 ( 1) link_BETA1-4 : angle 1.74962 ( 3) hydrogen bonds : bond 0.03645 ( 482) hydrogen bonds : angle 5.86717 ( 1383) SS BOND : bond 0.00503 ( 29) SS BOND : angle 0.97606 ( 58) covalent geometry : bond 0.00305 (19049) covalent geometry : angle 0.63426 (26062) *********************** 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 232 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 2.303 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: symmetry clash REVERT: A 364 LYS cc_start: 0.8249 (pttt) cc_final: 0.7624 (mmmt) REVERT: A 445 LYS cc_start: 0.8276 (mttt) cc_final: 0.7966 (mtmm) REVERT: B 376 ASP cc_start: 0.8581 (p0) cc_final: 0.8244 (p0) REVERT: C 348 PHE cc_start: 0.8583 (m-80) cc_final: 0.8374 (m-10) REVERT: F 568 MET cc_start: 0.6781 (tpp) cc_final: 0.5660 (tpt) REVERT: G 375 TYR cc_start: 0.8274 (m-10) cc_final: 0.7938 (m-10) REVERT: G 553 ASP cc_start: 0.7956 (t0) cc_final: 0.7755 (t70) REVERT: H 391 LYS cc_start: 0.8073 (tptt) cc_final: 0.7851 (tptp) REVERT: H 568 MET cc_start: 0.7622 (mtt) cc_final: 0.7215 (tmm) REVERT: J 31 ASP cc_start: 0.8771 (m-30) cc_final: 0.8540 (m-30) REVERT: K 467 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7587 (tpt90) REVERT: K 568 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7194 (mtt) REVERT: L 506 MET cc_start: 0.8415 (mpp) cc_final: 0.8164 (mpp) REVERT: L 515 TYR cc_start: 0.7822 (m-80) cc_final: 0.7399 (m-10) REVERT: L 534 TYR cc_start: 0.8786 (m-10) cc_final: 0.8240 (m-10) outliers start: 48 outliers final: 29 residues processed: 217 average time/residue: 0.4323 time to fit residues: 140.0443 Evaluate side-chains 202 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 489 MET Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE 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 G 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 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 35 ILE 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 Chi-restraints excluded: chain K residue 568 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 55 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.059800 restraints weight = 66388.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061698 restraints weight = 37576.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.062871 restraints weight = 27373.353| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19090 Z= 0.161 Angle : 0.647 10.694 26156 Z= 0.330 Chirality : 0.046 0.151 3095 Planarity : 0.004 0.048 3327 Dihedral : 4.507 28.072 2801 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.00 % Favored : 90.91 % Rotamer: Outliers : 2.70 % Allowed : 17.93 % Favored : 79.38 % 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: -1.52 (0.17), residues: 2344 helix: -1.44 (0.29), residues: 251 sheet: 0.28 (0.18), residues: 830 loop : -1.87 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 528 HIS 0.006 0.001 HIS C 430 PHE 0.021 0.002 PHE L 479 TYR 0.015 0.001 TYR F 375 ARG 0.004 0.000 ARG E 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 11) link_NAG-ASN : angle 1.68553 ( 33) link_BETA1-4 : bond 0.00386 ( 1) link_BETA1-4 : angle 1.68248 ( 3) hydrogen bonds : bond 0.03658 ( 482) hydrogen bonds : angle 5.68587 ( 1383) SS BOND : bond 0.00514 ( 29) SS BOND : angle 1.08626 ( 58) covalent geometry : bond 0.00383 (19049) covalent geometry : angle 0.64306 (26062) *********************** 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 239 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 2.075 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: 0.8395 (pttt) cc_final: 0.7713 (mmmt) REVERT: A 445 LYS cc_start: 0.8216 (mttt) cc_final: 0.7965 (mtmm) REVERT: B 376 ASP cc_start: 0.8434 (p0) cc_final: 0.8092 (p0) REVERT: E 506 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6668 (mtm) REVERT: G 375 TYR cc_start: 0.8254 (m-10) cc_final: 0.7876 (m-10) REVERT: G 385 GLN cc_start: 0.6143 (mm110) cc_final: 0.5810 (mm-40) REVERT: H 391 LYS cc_start: 0.8188 (tptt) cc_final: 0.7943 (tptp) REVERT: H 568 MET cc_start: 0.7534 (mtt) cc_final: 0.6931 (tmm) REVERT: J 31 ASP cc_start: 0.8718 (m-30) cc_final: 0.8198 (m-30) REVERT: K 558 LYS cc_start: 0.5932 (mppt) cc_final: 0.5600 (mppt) REVERT: K 568 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7254 (mtt) REVERT: L 534 TYR cc_start: 0.8776 (m-10) cc_final: 0.8278 (m-10) outliers start: 57 outliers final: 42 residues processed: 221 average time/residue: 0.3491 time to fit residues: 113.3007 Evaluate side-chains 208 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 A residue 538 VAL 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 473 THR Chi-restraints excluded: chain C residue 506 MET 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 491 ARG Chi-restraints excluded: chain D residue 533 THR 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 506 MET 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 472 ILE 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 395 ASN Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR 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 568 MET Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 222 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** B 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** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.087991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.056168 restraints weight = 68366.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058031 restraints weight = 38425.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059093 restraints weight = 28060.766| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 19090 Z= 0.339 Angle : 0.812 15.917 26156 Z= 0.418 Chirality : 0.051 0.219 3095 Planarity : 0.006 0.053 3327 Dihedral : 5.444 35.920 2801 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.58 % Favored : 89.29 % Rotamer: Outliers : 3.88 % Allowed : 17.36 % Favored : 78.76 % 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: -1.93 (0.17), residues: 2344 helix: -1.69 (0.28), residues: 244 sheet: -0.24 (0.18), residues: 858 loop : -1.99 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 488 HIS 0.012 0.002 HIS L 518 PHE 0.039 0.003 PHE D 479 TYR 0.021 0.002 TYR E 375 ARG 0.013 0.001 ARG C 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 11) link_NAG-ASN : angle 2.50055 ( 33) link_BETA1-4 : bond 0.00258 ( 1) link_BETA1-4 : angle 1.79435 ( 3) hydrogen bonds : bond 0.04712 ( 482) hydrogen bonds : angle 6.05573 ( 1383) SS BOND : bond 0.00777 ( 29) SS BOND : angle 1.80760 ( 58) covalent geometry : bond 0.00802 (19049) covalent geometry : angle 0.80410 (26062) *********************** 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 248 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 166 time to evaluate : 2.394 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: 0.8525 (pttt) cc_final: 0.7761 (mmmt) REVERT: A 445 LYS cc_start: 0.8223 (mttt) cc_final: 0.7901 (mtmm) REVERT: A 456 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 376 ASP cc_start: 0.8551 (p0) cc_final: 0.8226 (p0) REVERT: B 419 ASN cc_start: 0.9525 (t0) cc_final: 0.9244 (t0) REVERT: C 443 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6415 (ptt-90) REVERT: D 445 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7269 (mmtm) REVERT: E 358 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: F 527 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8795 (tp30) REVERT: G 385 GLN cc_start: 0.6091 (mm110) cc_final: 0.5726 (mm-40) REVERT: H 391 LYS cc_start: 0.8244 (tptt) cc_final: 0.7956 (tptp) REVERT: J 31 ASP cc_start: 0.8774 (m-30) cc_final: 0.8337 (m-30) REVERT: L 534 TYR cc_start: 0.9025 (m-10) cc_final: 0.8608 (m-10) outliers start: 82 outliers final: 64 residues processed: 230 average time/residue: 0.3387 time to fit residues: 115.7798 Evaluate side-chains 220 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 533 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 443 ARG Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 484 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 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 358 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 506 MET 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 456 LEU 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 347 VAL Chi-restraints excluded: chain G residue 472 ILE 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 396 ILE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 364 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 210 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 180 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 0.0010 chunk 41 optimal weight: 0.7980 overall best weight: 0.5686 ------------------------------------------------------------------------------- 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** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN H 395 ASN ** H 540 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.090756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059211 restraints weight = 66704.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061213 restraints weight = 36636.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062401 restraints weight = 26459.881| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19090 Z= 0.127 Angle : 0.671 12.314 26156 Z= 0.338 Chirality : 0.046 0.184 3095 Planarity : 0.005 0.052 3327 Dihedral : 4.773 30.784 2801 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.98 % Favored : 91.89 % Rotamer: Outliers : 2.65 % Allowed : 19.30 % Favored : 78.05 % 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: -1.58 (0.17), residues: 2344 helix: -1.28 (0.30), residues: 244 sheet: 0.05 (0.18), residues: 842 loop : -1.83 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 528 HIS 0.016 0.001 HIS I 123 PHE 0.021 0.001 PHE L 479 TYR 0.018 0.001 TYR E 375 ARG 0.011 0.001 ARG C 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 11) link_NAG-ASN : angle 1.50714 ( 33) link_BETA1-4 : bond 0.00049 ( 1) link_BETA1-4 : angle 1.48051 ( 3) hydrogen bonds : bond 0.03318 ( 482) hydrogen bonds : angle 5.57218 ( 1383) SS BOND : bond 0.00662 ( 29) SS BOND : angle 1.13714 ( 58) covalent geometry : bond 0.00290 (19049) covalent geometry : angle 0.66766 (26062) *********************** REFINEMENT MACRO_CYCLE 7 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 228 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 3.448 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: A 364 LYS cc_start: 0.8407 (pttt) cc_final: 0.7656 (mmmt) REVERT: A 404 THR cc_start: 0.5899 (OUTLIER) cc_final: 0.5624 (t) REVERT: A 445 LYS cc_start: 0.8297 (mttt) cc_final: 0.7986 (mtmm) REVERT: B 376 ASP cc_start: 0.8511 (p0) cc_final: 0.8183 (p0) REVERT: B 419 ASN cc_start: 0.9433 (t0) cc_final: 0.9117 (t0) REVERT: D 445 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7328 (mmtm) REVERT: E 364 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8673 (mmtm) REVERT: E 506 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: G 375 TYR cc_start: 0.8427 (m-80) cc_final: 0.8022 (m-10) REVERT: H 391 LYS cc_start: 0.8131 (tptt) cc_final: 0.7898 (tptp) REVERT: H 568 MET cc_start: 0.7543 (mtt) cc_final: 0.7254 (tmm) REVERT: J 31 ASP cc_start: 0.8715 (m-30) cc_final: 0.8283 (m-30) REVERT: L 534 TYR cc_start: 0.8928 (m-10) cc_final: 0.8539 (m-10) outliers start: 56 outliers final: 41 residues processed: 215 average time/residue: 0.3852 time to fit residues: 123.0933 Evaluate side-chains 202 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR 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 A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 506 MET 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 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 533 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 506 MET 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 456 LEU 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 395 ASN Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 85 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 364 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 104 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.090336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058840 restraints weight = 66864.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060818 restraints weight = 36879.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062060 restraints weight = 26633.721| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19090 Z= 0.143 Angle : 0.679 12.284 26156 Z= 0.341 Chirality : 0.046 0.158 3095 Planarity : 0.005 0.048 3327 Dihedral : 4.648 29.404 2801 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.92 % Favored : 90.96 % Rotamer: Outliers : 2.84 % Allowed : 19.68 % Favored : 77.48 % 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: -1.48 (0.17), residues: 2344 helix: -1.18 (0.30), residues: 244 sheet: 0.14 (0.18), residues: 831 loop : -1.77 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 418 HIS 0.007 0.001 HIS K 400 PHE 0.019 0.001 PHE L 479 TYR 0.023 0.001 TYR L 515 ARG 0.012 0.001 ARG C 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 11) link_NAG-ASN : angle 1.62467 ( 33) link_BETA1-4 : bond 0.00160 ( 1) link_BETA1-4 : angle 1.51411 ( 3) hydrogen bonds : bond 0.03352 ( 482) hydrogen bonds : angle 5.48933 ( 1383) SS BOND : bond 0.00503 ( 29) SS BOND : angle 1.13469 ( 58) covalent geometry : bond 0.00339 (19049) covalent geometry : angle 0.67528 (26062) *********************** REFINEMENT MACRO_CYCLE 8 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 225 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 2.305 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: A 364 LYS cc_start: 0.8413 (pttt) cc_final: 0.7634 (mmmt) REVERT: A 404 THR cc_start: 0.5912 (OUTLIER) cc_final: 0.5618 (t) REVERT: A 445 LYS cc_start: 0.8296 (mttt) cc_final: 0.7964 (mtmm) REVERT: B 376 ASP cc_start: 0.8466 (p0) cc_final: 0.8131 (p0) REVERT: B 419 ASN cc_start: 0.9434 (t0) cc_final: 0.9091 (t0) REVERT: D 445 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7266 (mmtm) REVERT: E 358 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: E 364 LYS cc_start: 0.9027 (mtmm) cc_final: 0.8600 (mmtm) REVERT: E 506 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6876 (mtm) REVERT: G 375 TYR cc_start: 0.8402 (m-80) cc_final: 0.7986 (m-10) REVERT: G 385 GLN cc_start: 0.5038 (mm-40) cc_final: 0.4630 (mm-40) REVERT: H 391 LYS cc_start: 0.8145 (tptt) cc_final: 0.7912 (tptp) REVERT: H 568 MET cc_start: 0.7420 (mtt) cc_final: 0.7145 (tmm) REVERT: J 31 ASP cc_start: 0.8682 (m-30) cc_final: 0.8239 (m-30) REVERT: L 524 SER cc_start: 0.8537 (m) cc_final: 0.8084 (t) REVERT: L 534 TYR cc_start: 0.8950 (m-10) cc_final: 0.8484 (m-10) outliers start: 60 outliers final: 46 residues processed: 214 average time/residue: 0.3673 time to fit residues: 117.1953 Evaluate side-chains 206 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR 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 A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 358 PHE 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 506 MET Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 392 THR 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 441 ILE 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 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 364 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain L residue 520 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 225 optimal weight: 0.0050 chunk 108 optimal weight: 3.9990 chunk 201 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 0.0270 chunk 73 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 overall best weight: 0.3652 ------------------------------------------------------------------------------- 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 C 545 ASN G 463 GLN I 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.091212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.060258 restraints weight = 66748.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.062028 restraints weight = 39488.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063100 restraints weight = 29276.240| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19090 Z= 0.117 Angle : 0.660 11.210 26156 Z= 0.331 Chirality : 0.046 0.162 3095 Planarity : 0.004 0.048 3327 Dihedral : 4.406 25.461 2801 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.72 % Favored : 92.19 % Rotamer: Outliers : 2.70 % Allowed : 19.87 % Favored : 77.44 % 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: -1.28 (0.17), residues: 2344 helix: -1.00 (0.31), residues: 244 sheet: 0.29 (0.18), residues: 833 loop : -1.66 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 418 HIS 0.006 0.001 HIS K 400 PHE 0.020 0.001 PHE L 479 TYR 0.021 0.001 TYR L 515 ARG 0.006 0.000 ARG I 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 11) link_NAG-ASN : angle 1.29272 ( 33) link_BETA1-4 : bond 0.00537 ( 1) link_BETA1-4 : angle 1.42393 ( 3) hydrogen bonds : bond 0.02993 ( 482) hydrogen bonds : angle 5.29478 ( 1383) SS BOND : bond 0.00450 ( 29) SS BOND : angle 0.92447 ( 58) covalent geometry : bond 0.00270 (19049) covalent geometry : angle 0.65785 (26062) *********************** REFINEMENT MACRO_CYCLE 9 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 to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 2.276 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: 0.8260 (pttt) cc_final: 0.7354 (mmtt) REVERT: A 445 LYS cc_start: 0.8264 (mttt) cc_final: 0.7953 (mtmm) REVERT: B 376 ASP cc_start: 0.8518 (p0) cc_final: 0.8185 (p0) REVERT: B 419 ASN cc_start: 0.9442 (t0) cc_final: 0.9105 (t0) REVERT: D 445 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7359 (mmtm) REVERT: E 358 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: G 375 TYR cc_start: 0.8406 (m-80) cc_final: 0.7985 (m-10) REVERT: G 385 GLN cc_start: 0.4854 (mm-40) cc_final: 0.4454 (mm-40) REVERT: H 391 LYS cc_start: 0.8107 (tptt) cc_final: 0.7893 (tptp) REVERT: I 121 ASN cc_start: 0.8948 (m110) cc_final: 0.8146 (t0) REVERT: J 31 ASP cc_start: 0.8674 (m-30) cc_final: 0.8251 (m-30) REVERT: L 524 SER cc_start: 0.8573 (m) cc_final: 0.8182 (t) REVERT: L 534 TYR cc_start: 0.8848 (m-10) cc_final: 0.8467 (m-10) outliers start: 57 outliers final: 46 residues processed: 222 average time/residue: 0.3412 time to fit residues: 113.3295 Evaluate side-chains 204 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 538 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE 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 373 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 G residue 392 THR 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 537 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 364 LYS Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 64 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 203 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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** F 430 HIS H 395 ASN ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 HIS ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.089887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058756 restraints weight = 66679.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.061589 restraints weight = 42551.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.061795 restraints weight = 26927.327| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19090 Z= 0.161 Angle : 0.688 11.675 26156 Z= 0.347 Chirality : 0.046 0.151 3095 Planarity : 0.005 0.046 3327 Dihedral : 4.491 25.847 2801 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.58 % Favored : 91.30 % Rotamer: Outliers : 2.51 % Allowed : 20.34 % Favored : 77.15 % 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: -1.30 (0.17), residues: 2344 helix: -0.90 (0.32), residues: 242 sheet: 0.25 (0.18), residues: 844 loop : -1.69 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 418 HIS 0.006 0.001 HIS K 400 PHE 0.023 0.002 PHE L 479 TYR 0.017 0.002 TYR K 375 ARG 0.007 0.001 ARG H 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 11) link_NAG-ASN : angle 1.69143 ( 33) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 1.47795 ( 3) hydrogen bonds : bond 0.03335 ( 482) hydrogen bonds : angle 5.34396 ( 1383) SS BOND : bond 0.00513 ( 29) SS BOND : angle 1.17936 ( 58) covalent geometry : bond 0.00383 (19049) covalent geometry : angle 0.68366 (26062) ********************** REFINEMENT MACRO_CYCLE 10 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 213 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 2.283 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: A 364 LYS cc_start: 0.8263 (pttt) cc_final: 0.7348 (mmtt) REVERT: A 404 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.5692 (t) REVERT: A 445 LYS cc_start: 0.8352 (mttt) cc_final: 0.8019 (mtmm) REVERT: B 359 LEU cc_start: 0.9095 (tp) cc_final: 0.8848 (pp) REVERT: B 376 ASP cc_start: 0.8540 (p0) cc_final: 0.8219 (p0) REVERT: B 419 ASN cc_start: 0.9538 (t0) cc_final: 0.9255 (t0) REVERT: B 570 ASP cc_start: 0.7693 (m-30) cc_final: 0.7386 (m-30) REVERT: D 445 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7649 (mmtm) REVERT: E 358 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: G 375 TYR cc_start: 0.8423 (m-80) cc_final: 0.7707 (m-80) REVERT: H 391 LYS cc_start: 0.8112 (tptt) cc_final: 0.7885 (tptp) REVERT: J 31 ASP cc_start: 0.8724 (m-30) cc_final: 0.8365 (m-30) REVERT: L 524 SER cc_start: 0.8604 (m) cc_final: 0.8156 (t) REVERT: L 534 TYR cc_start: 0.9035 (m-10) cc_final: 0.8619 (m-10) outliers start: 53 outliers final: 48 residues processed: 206 average time/residue: 0.3454 time to fit residues: 106.8288 Evaluate side-chains 207 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 THR 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 523 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 400 HIS Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain E residue 358 PHE 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 537 VAL Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 392 THR 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 395 ASN Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 70 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 195 optimal weight: 0.0170 chunk 220 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 139 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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** F 430 HIS ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.089893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058844 restraints weight = 66825.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060584 restraints weight = 39759.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061589 restraints weight = 29694.265| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 19090 Z= 0.185 Angle : 0.832 59.027 26156 Z= 0.459 Chirality : 0.048 0.890 3095 Planarity : 0.005 0.046 3327 Dihedral : 4.489 25.859 2801 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.34 % Rotamer: Outliers : 2.60 % Allowed : 20.20 % Favored : 77.20 % Cbeta Deviations : 0.04 % 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: -1.30 (0.17), residues: 2344 helix: -0.89 (0.32), residues: 242 sheet: 0.25 (0.18), residues: 844 loop : -1.69 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 418 HIS 0.005 0.001 HIS K 400 PHE 0.022 0.001 PHE L 479 TYR 0.017 0.001 TYR C 562 ARG 0.024 0.001 ARG E 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 11) link_NAG-ASN : angle 1.71090 ( 33) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 1.52175 ( 3) hydrogen bonds : bond 0.03292 ( 482) hydrogen bonds : angle 5.34119 ( 1383) SS BOND : bond 0.00516 ( 29) SS BOND : angle 1.13136 ( 58) covalent geometry : bond 0.00407 (19049) covalent geometry : angle 0.82893 (26062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8897.84 seconds wall clock time: 156 minutes 32.30 seconds (9392.30 seconds total)