Starting phenix.real_space_refine on Sun Aug 24 11:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytc_34085/08_2025/7ytc_34085.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.049 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 95 5.16 5 C 12167 2.51 5 N 3276 2.21 5 O 3790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19328 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} 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: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 825 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: "J" 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: 5.74, per 1000 atoms: 0.30 Number of scatterers: 19328 At special positions: 0 Unit cell: (116.748, 189.612, 163.116, 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 95 16.00 O 3790 8.00 N 3276 7.00 C 12167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, 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 B 367 " - pdb=" SG CYS B 426 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.05 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.04 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 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=2.03 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 J 12 " - pdb=" SG CYS J 100 " distance=2.03 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 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 Atom "HETATM19284 O5 NAG H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied 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 J 201 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 968.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 60 sheets defined 9.4% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.587A pdb=" N ASN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.957A pdb=" N THR A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.606A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.058A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 4.015A pdb=" N GLY B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.718A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 467 removed outlier: 3.550A pdb=" N ARG C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.799A pdb=" N THR C 530 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 4.267A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 460 through 467 removed outlier: 4.113A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 529 removed outlier: 3.861A pdb=" N TRP D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 529 " --> pdb=" O GLU D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 529' Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.078A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 419' Processing helix chain 'F' and resid 524 through 529 removed outlier: 3.608A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.817A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 524 through 530 removed outlier: 4.023A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN G 529 " --> pdb=" O GLU G 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 524 through 530' Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.954A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 415 through 419 removed outlier: 4.192A pdb=" N ASN H 419 " --> pdb=" O ASP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 530 removed outlier: 3.514A pdb=" N THR H 530 " --> pdb=" O GLU H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.590A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'K' and resid 414 through 419 removed outlier: 4.134A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 414 through 419' Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 525 through 529 removed outlier: 3.852A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 525 through 529' Processing helix chain 'L' and resid 353 through 358 removed outlier: 3.673A pdb=" N PHE L 358 " --> pdb=" O PHE L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 420 removed outlier: 4.013A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 525 through 530 Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.537A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.586A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.791A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.975A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AB5, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB8, first strand: chain 'D' and resid 346 through 350 removed outlier: 4.120A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.706A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'D' and resid 565 through 567 removed outlier: 7.240A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 346 through 350 Processing sheet with id=AC6, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.656A pdb=" N LEU E 437 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 removed outlier: 3.736A pdb=" N GLN E 493 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD2, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (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 565 through 567 Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.816A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN G 490 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 346 through 350 Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.742A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (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 566 through 567 Processing sheet with id=AF1, first strand: chain 'J' and resid 21 through 22 removed outlier: 4.432A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF3, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.688A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AF5, first strand: chain 'K' and resid 379 through 384 Processing sheet with id=AF6, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.660A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF8, first strand: chain 'K' and resid 506 through 507 Processing sheet with id=AF9, first strand: chain 'K' and resid 561 through 562 removed outlier: 6.346A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 346 through 350 Processing sheet with id=AG2, first strand: chain 'L' and resid 380 through 383 removed outlier: 4.090A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 454 through 457 removed outlier: 4.038A pdb=" N GLY L 478 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 493 through 495 removed outlier: 4.278A pdb=" N TRP L 488 " --> pdb=" O LEU L 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 539 " --> pdb=" O PHE L 485 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 33 through 37 removed outlier: 4.203A pdb=" N LEU R 86 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR R 81 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 58 through 62 removed outlier: 5.362A pdb=" N THR R 60 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG R 50 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR R 47 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN R 116 " --> pdb=" O CYS R 104 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1494 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: 4.71 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3154 1.25 - 1.40: 4597 1.40 - 1.54: 11748 1.54 - 1.68: 174 1.68 - 1.83: 129 Bond restraints: 19802 Sorted by residual: bond pdb=" CA ASN H 563 " pdb=" C ASN H 563 " ideal model delta sigma weight residual 1.524 1.389 0.134 1.30e-02 5.92e+03 1.07e+02 bond pdb=" C ASN H 563 " pdb=" O ASN H 563 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.22e-02 6.72e+03 1.02e+02 bond pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 1.520 1.406 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C ILE J 39 " pdb=" O ILE J 39 " ideal model delta sigma weight residual 1.238 1.137 0.100 1.06e-02 8.90e+03 8.98e+01 bond pdb=" C VAL C 564 " pdb=" O VAL C 564 " ideal model delta sigma weight residual 1.237 1.146 0.091 9.80e-03 1.04e+04 8.59e+01 ... (remaining 19797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 26622 4.39 - 8.79: 395 8.79 - 13.18: 53 13.18 - 17.57: 20 17.57 - 21.97: 3 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N THR B 533 " pdb=" CA THR B 533 " pdb=" C THR B 533 " ideal model delta sigma weight residual 111.28 133.25 -21.97 1.09e+00 8.42e-01 4.06e+02 angle pdb=" N THR K 533 " pdb=" CA THR K 533 " pdb=" C THR K 533 " ideal model delta sigma weight residual 111.28 127.21 -15.93 1.09e+00 8.42e-01 2.14e+02 angle pdb=" C SER L 496 " pdb=" N PRO L 497 " pdb=" CA PRO L 497 " ideal model delta sigma weight residual 119.87 134.35 -14.48 1.04e+00 9.25e-01 1.94e+02 angle pdb=" C LYS F 558 " pdb=" N PRO F 559 " pdb=" CA PRO F 559 " ideal model delta sigma weight residual 119.05 134.25 -15.20 1.11e+00 8.12e-01 1.88e+02 angle pdb=" N PRO B 452 " pdb=" CA PRO B 452 " pdb=" C PRO B 452 " ideal model delta sigma weight residual 113.84 130.83 -16.99 1.30e+00 5.92e-01 1.71e+02 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 11027 21.57 - 43.15: 902 43.15 - 64.72: 217 64.72 - 86.29: 40 86.29 - 107.87: 10 Dihedral angle restraints: 12196 sinusoidal: 4949 harmonic: 7247 Sorted by residual: dihedral pdb=" C THR F 560 " pdb=" N THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual -122.00 -151.55 29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual 123.40 151.69 -28.29 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C ASN R 85 " pdb=" N ASN R 85 " pdb=" CA ASN R 85 " pdb=" CB ASN R 85 " ideal model delta harmonic sigma weight residual -122.60 -146.78 24.18 0 2.50e+00 1.60e-01 9.36e+01 ... (remaining 12193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3161 0.270 - 0.540: 51 0.540 - 0.809: 7 0.809 - 1.079: 1 1.079 - 1.349: 1 Chirality restraints: 3221 Sorted by residual: chirality pdb=" CA THR F 560 " pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CB THR F 560 " both_signs ideal model delta sigma weight residual False 2.53 1.18 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA ASN R 85 " pdb=" N ASN R 85 " pdb=" C ASN R 85 " pdb=" CB ASN R 85 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA THR B 533 " pdb=" N THR B 533 " pdb=" C THR B 533 " pdb=" CB THR B 533 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3218 not shown) Planarity restraints: 3467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 558 " -0.101 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO K 559 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO K 559 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO K 559 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 562 " 0.030 2.00e-02 2.50e+03 5.98e-02 3.57e+01 pdb=" C TYR C 562 " -0.103 2.00e-02 2.50e+03 pdb=" O TYR C 562 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN C 563 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 488 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C TRP B 488 " -0.095 2.00e-02 2.50e+03 pdb=" O TRP B 488 " 0.036 2.00e-02 2.50e+03 pdb=" N MET B 489 " 0.033 2.00e-02 2.50e+03 ... (remaining 3464 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 28 1.95 - 2.68: 1065 2.68 - 3.42: 25865 3.42 - 4.16: 44293 4.16 - 4.90: 76988 Nonbonded interactions: 148239 Sorted by model distance: nonbonded pdb=" NH1 ARG C 384 " pdb=" O ALA C 389 " model vdw 1.208 3.120 nonbonded pdb=" O ARG L 491 " pdb=" NE2 GLN L 493 " model vdw 1.411 3.120 nonbonded pdb=" OD2 ASP E 453 " pdb=" CE2 TYR E 455 " model vdw 1.433 3.340 nonbonded pdb=" OD2 ASP E 453 " pdb=" CZ TYR E 455 " model vdw 1.501 3.260 nonbonded pdb=" OD1 ASN C 386 " pdb=" CG GLU C 388 " model vdw 1.537 3.440 ... (remaining 148234 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 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 22.320 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.011 0.246 19841 Z= 0.733 Angle : 1.397 37.574 27182 Z= 0.841 Chirality : 0.087 1.349 3221 Planarity : 0.008 0.151 3456 Dihedral : 16.748 107.868 7388 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer: Outliers : 8.45 % Allowed : 3.41 % Favored : 88.15 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.16), residues: 2438 helix: -2.45 (0.36), residues: 151 sheet: -0.93 (0.17), residues: 897 loop : -2.01 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 451 TYR 0.047 0.003 TYR J 101 PHE 0.079 0.002 PHE G 479 TRP 0.022 0.002 TRP G 528 HIS 0.016 0.001 HIS D 450 Details of bonding type rmsd covalent geometry : bond 0.01066 (19802) covalent geometry : angle 1.32177 (27093) SS BOND : bond 0.00836 ( 28) SS BOND : angle 2.24040 ( 56) hydrogen bonds : bond 0.19892 ( 532) hydrogen bonds : angle 8.25738 ( 1494) link_NAG-ASN : bond 0.08924 ( 11) link_NAG-ASN : angle 12.82384 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 312 time to evaluate : 0.895 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: B 415 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: C 416 ASP cc_start: 0.9239 (m-30) cc_final: 0.9033 (p0) REVERT: C 566 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8664 (pp) REVERT: D 424 PHE cc_start: 0.8515 (m-80) cc_final: 0.8263 (m-80) REVERT: D 534 TYR cc_start: 0.7701 (m-80) cc_final: 0.7359 (m-10) REVERT: E 500 TYR cc_start: 0.8833 (p90) cc_final: 0.8493 (p90) REVERT: E 503 SER cc_start: 0.8521 (t) cc_final: 0.8291 (m) REVERT: F 424 PHE cc_start: 0.7438 (m-80) cc_final: 0.7179 (m-80) REVERT: F 449 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7482 (pp) REVERT: F 451 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8147 (mtm-85) REVERT: G 364 LYS cc_start: 0.8110 (tptt) cc_final: 0.7738 (tppt) REVERT: G 490 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6360 (tp40) REVERT: H 566 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8629 (mp) REVERT: J 9 ASP cc_start: 0.7874 (t70) cc_final: 0.7461 (t70) REVERT: K 463 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7800 (tm-30) REVERT: K 530 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.5850 (t) REVERT: K 554 LYS cc_start: 0.8667 (tttt) cc_final: 0.8341 (tttm) REVERT: L 450 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5654 (m90) REVERT: L 451 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: L 486 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8441 (t) REVERT: L 500 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.6152 (p90) REVERT: L 514 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.4898 (ptp90) REVERT: L 570 ASP cc_start: 0.7952 (t0) cc_final: 0.7696 (t0) REVERT: R 50 ARG cc_start: 0.7388 (ttt180) cc_final: 0.7006 (ttp80) REVERT: R 109 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7839 (t0) outliers start: 186 outliers final: 98 residues processed: 464 average time/residue: 0.1811 time to fit residues: 119.6256 Evaluate side-chains 359 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 248 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 PRO Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 562 TYR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 485 PHE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 451 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 529 ASN Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 500 TYR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 87 PHE Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 ASN Chi-restraints excluded: chain R residue 123 HIS Chi-restraints excluded: chain R residue 124 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 439 GLN C 450 HIS F 450 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN H 430 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.205014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.124932 restraints weight = 27280.786| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.87 r_work: 0.3409 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19841 Z= 0.151 Angle : 0.722 12.776 27182 Z= 0.361 Chirality : 0.050 0.410 3221 Planarity : 0.006 0.084 3456 Dihedral : 11.131 85.555 3110 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 4.72 % Allowed : 10.94 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.16), residues: 2438 helix: -2.45 (0.32), residues: 160 sheet: -0.76 (0.17), residues: 907 loop : -2.02 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.029 0.002 TYR C 534 PHE 0.025 0.002 PHE B 348 TRP 0.029 0.002 TRP H 382 HIS 0.008 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00344 (19802) covalent geometry : angle 0.69848 (27093) SS BOND : bond 0.00425 ( 28) SS BOND : angle 1.13884 ( 56) hydrogen bonds : bond 0.04036 ( 532) hydrogen bonds : angle 6.35372 ( 1494) link_NAG-ASN : bond 0.01099 ( 11) link_NAG-ASN : angle 5.11772 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 289 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7516 (pptt) REVERT: B 461 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7258 (tpp-160) REVERT: B 489 MET cc_start: 0.8225 (mtt) cc_final: 0.7859 (mtt) REVERT: B 490 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: B 510 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: B 546 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7657 (ttm170) REVERT: D 489 MET cc_start: 0.8235 (mtm) cc_final: 0.7788 (mtt) REVERT: D 498 GLU cc_start: 0.8774 (pt0) cc_final: 0.8295 (pm20) REVERT: E 453 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6916 (p0) REVERT: E 500 TYR cc_start: 0.9056 (p90) cc_final: 0.8749 (p90) REVERT: E 514 ARG cc_start: 0.8287 (mtt90) cc_final: 0.8085 (mpp80) REVERT: E 554 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7458 (tmtt) REVERT: F 449 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7779 (pp) REVERT: F 453 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7277 (p0) REVERT: F 461 ARG cc_start: 0.7754 (mpp80) cc_final: 0.7291 (mtt180) REVERT: G 443 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7738 (ptm-80) REVERT: H 562 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7014 (p90) REVERT: J 9 ASP cc_start: 0.8234 (t70) cc_final: 0.7767 (t70) REVERT: J 16 ARG cc_start: 0.8098 (tmt170) cc_final: 0.7318 (tmt170) REVERT: J 106 ASN cc_start: 0.7739 (p0) cc_final: 0.7419 (m-40) REVERT: K 530 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6467 (t) REVERT: K 554 LYS cc_start: 0.8339 (tttt) cc_final: 0.7941 (tttm) REVERT: L 450 HIS cc_start: 0.6209 (OUTLIER) cc_final: 0.5701 (m90) REVERT: L 451 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7616 (ttm170) REVERT: L 489 MET cc_start: 0.7164 (mtp) cc_final: 0.6344 (mtp) REVERT: L 518 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6632 (t-170) REVERT: R 73 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8112 (mmmt) REVERT: R 109 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7620 (t0) REVERT: R 121 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6912 (t0) outliers start: 104 outliers final: 55 residues processed: 361 average time/residue: 0.1814 time to fit residues: 93.3479 Evaluate side-chains 314 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 TRP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 172 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN B 419 ASN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN C 463 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 465 ASN L 493 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.202079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121859 restraints weight = 27314.675| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.16 r_work: 0.3332 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19841 Z= 0.184 Angle : 0.701 12.894 27182 Z= 0.347 Chirality : 0.049 0.389 3221 Planarity : 0.005 0.071 3456 Dihedral : 8.817 77.086 2974 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.85 % Rotamer: Outliers : 4.18 % Allowed : 14.85 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.16), residues: 2438 helix: -2.27 (0.34), residues: 166 sheet: -0.66 (0.17), residues: 891 loop : -2.01 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 443 TYR 0.019 0.002 TYR K 534 PHE 0.020 0.002 PHE B 348 TRP 0.012 0.001 TRP B 382 HIS 0.004 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00436 (19802) covalent geometry : angle 0.67454 (27093) SS BOND : bond 0.00381 ( 28) SS BOND : angle 1.29355 ( 56) hydrogen bonds : bond 0.03699 ( 532) hydrogen bonds : angle 5.95250 ( 1494) link_NAG-ASN : bond 0.00880 ( 11) link_NAG-ASN : angle 5.28723 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 259 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7674 (pptt) REVERT: B 461 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7377 (tpp-160) REVERT: B 489 MET cc_start: 0.8362 (mtt) cc_final: 0.7975 (mtt) REVERT: B 490 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: B 533 THR cc_start: 0.7889 (m) cc_final: 0.7549 (t) REVERT: B 534 TYR cc_start: 0.8459 (m-80) cc_final: 0.8219 (m-80) REVERT: D 489 MET cc_start: 0.8434 (mtm) cc_final: 0.7880 (mtt) REVERT: E 391 LYS cc_start: 0.7682 (tptp) cc_final: 0.7115 (ttpt) REVERT: E 440 THR cc_start: 0.5203 (OUTLIER) cc_final: 0.4780 (p) REVERT: E 449 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8465 (mm) REVERT: E 453 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7111 (p0) REVERT: E 514 ARG cc_start: 0.8453 (mtt90) cc_final: 0.8186 (mpp80) REVERT: E 554 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7489 (tmtt) REVERT: F 449 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7830 (pp) REVERT: F 453 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7725 (p0) REVERT: F 461 ARG cc_start: 0.7969 (mpp80) cc_final: 0.7464 (mtt180) REVERT: G 364 LYS cc_start: 0.7779 (tptt) cc_final: 0.7410 (tppt) REVERT: H 453 ASP cc_start: 0.8012 (t0) cc_final: 0.7805 (t0) REVERT: H 473 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8921 (p) REVERT: H 568 MET cc_start: 0.7302 (mmm) cc_final: 0.7057 (mmm) REVERT: J 106 ASN cc_start: 0.7849 (p0) cc_final: 0.7625 (m-40) REVERT: K 416 ASP cc_start: 0.7337 (p0) cc_final: 0.7068 (p0) REVERT: K 418 TRP cc_start: 0.6596 (OUTLIER) cc_final: 0.5598 (m-90) REVERT: K 514 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6958 (mtp85) REVERT: L 450 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5827 (m90) REVERT: L 451 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: L 514 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.4827 (ptp90) REVERT: L 518 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6618 (t-170) REVERT: R 75 ARG cc_start: 0.6289 (ptp90) cc_final: 0.5985 (ptt180) REVERT: R 109 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7472 (t0) outliers start: 92 outliers final: 57 residues processed: 321 average time/residue: 0.1772 time to fit residues: 81.8524 Evaluate side-chains 312 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 240 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 211 optimal weight: 20.0000 chunk 25 optimal weight: 50.0000 chunk 29 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 439 GLN B 510 GLN C 463 GLN C 545 ASN E 493 GLN G 450 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.201567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120401 restraints weight = 27379.655| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.80 r_work: 0.3342 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19841 Z= 0.172 Angle : 0.676 13.046 27182 Z= 0.333 Chirality : 0.048 0.385 3221 Planarity : 0.005 0.069 3456 Dihedral : 7.970 68.927 2952 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.70 % Favored : 91.22 % Rotamer: Outliers : 4.72 % Allowed : 16.62 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.16), residues: 2438 helix: -2.14 (0.35), residues: 165 sheet: -0.57 (0.17), residues: 874 loop : -1.97 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 461 TYR 0.018 0.001 TYR K 534 PHE 0.016 0.002 PHE E 424 TRP 0.014 0.001 TRP B 382 HIS 0.004 0.001 HIS H 518 Details of bonding type rmsd covalent geometry : bond 0.00408 (19802) covalent geometry : angle 0.64883 (27093) SS BOND : bond 0.00458 ( 28) SS BOND : angle 1.35231 ( 56) hydrogen bonds : bond 0.03448 ( 532) hydrogen bonds : angle 5.69762 ( 1494) link_NAG-ASN : bond 0.00846 ( 11) link_NAG-ASN : angle 5.31161 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 260 time to evaluate : 0.708 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: A 455 TYR cc_start: 0.8487 (m-80) cc_final: 0.8059 (m-80) REVERT: A 537 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8786 (m) REVERT: B 445 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7807 (pptt) REVERT: B 461 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7367 (tpp-160) REVERT: B 489 MET cc_start: 0.8372 (mtt) cc_final: 0.7952 (mtt) REVERT: B 490 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: B 510 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7839 (pp30) REVERT: B 533 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7485 (t) REVERT: C 441 ILE cc_start: 0.3635 (OUTLIER) cc_final: 0.2509 (mt) REVERT: C 469 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7770 (p) REVERT: D 489 MET cc_start: 0.8532 (mtm) cc_final: 0.7939 (mtt) REVERT: E 391 LYS cc_start: 0.7644 (tptp) cc_final: 0.7118 (ttpt) REVERT: E 440 THR cc_start: 0.5259 (OUTLIER) cc_final: 0.4511 (p) REVERT: E 449 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8422 (mm) REVERT: E 451 ARG cc_start: 0.8785 (ptm-80) cc_final: 0.8582 (ptm-80) REVERT: E 554 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7463 (tmtt) REVERT: F 449 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7875 (pp) REVERT: F 453 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7595 (p0) REVERT: G 364 LYS cc_start: 0.7859 (tptt) cc_final: 0.7604 (tppt) REVERT: G 443 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7332 (ptm-80) REVERT: G 445 LYS cc_start: 0.7957 (tptt) cc_final: 0.7522 (pttt) REVERT: H 380 ILE cc_start: 0.1410 (mm) cc_final: 0.1047 (tt) REVERT: H 453 ASP cc_start: 0.8037 (t0) cc_final: 0.7623 (t0) REVERT: H 568 MET cc_start: 0.7304 (mmm) cc_final: 0.7070 (mmm) REVERT: K 418 TRP cc_start: 0.6539 (OUTLIER) cc_final: 0.4190 (t-100) REVERT: K 451 ARG cc_start: 0.8547 (ptm-80) cc_final: 0.8159 (ptp-170) REVERT: K 463 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7573 (tm-30) REVERT: K 514 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.6901 (mtp85) REVERT: L 450 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.5706 (m90) REVERT: L 451 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: L 518 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6638 (t-170) REVERT: L 561 LEU cc_start: 0.8789 (tt) cc_final: 0.8268 (pp) REVERT: R 75 ARG cc_start: 0.6232 (ptp90) cc_final: 0.5922 (ptt180) REVERT: R 90 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7435 (tm-30) REVERT: R 109 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7300 (t0) REVERT: R 112 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7340 (ptm160) outliers start: 104 outliers final: 65 residues processed: 333 average time/residue: 0.1772 time to fit residues: 84.5132 Evaluate side-chains 323 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 241 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 414 CYS Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 235 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 40.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 430 HIS ** 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 = 0.4513 r_free = 0.4513 target = 0.201691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120680 restraints weight = 27173.046| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.82 r_work: 0.3346 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19841 Z= 0.154 Angle : 0.659 12.906 27182 Z= 0.324 Chirality : 0.048 0.382 3221 Planarity : 0.005 0.062 3456 Dihedral : 7.598 59.047 2948 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.65 % Favored : 91.26 % Rotamer: Outliers : 4.81 % Allowed : 17.57 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.17), residues: 2438 helix: -1.99 (0.35), residues: 164 sheet: -0.51 (0.17), residues: 879 loop : -1.89 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 384 TYR 0.016 0.001 TYR K 534 PHE 0.021 0.001 PHE L 516 TRP 0.018 0.001 TRP B 382 HIS 0.004 0.001 HIS H 518 Details of bonding type rmsd covalent geometry : bond 0.00365 (19802) covalent geometry : angle 0.63017 (27093) SS BOND : bond 0.00351 ( 28) SS BOND : angle 1.51227 ( 56) hydrogen bonds : bond 0.03291 ( 532) hydrogen bonds : angle 5.55383 ( 1494) link_NAG-ASN : bond 0.00844 ( 11) link_NAG-ASN : angle 5.29842 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 254 time to evaluate : 0.776 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 REVERT: A 455 TYR cc_start: 0.8477 (m-80) cc_final: 0.8157 (m-80) REVERT: B 445 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7872 (pptt) REVERT: B 461 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7400 (tpp-160) REVERT: B 466 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6862 (pp) REVERT: B 489 MET cc_start: 0.8366 (mtt) cc_final: 0.7952 (mtt) REVERT: B 490 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: B 510 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8082 (pp30) REVERT: B 533 THR cc_start: 0.7813 (m) cc_final: 0.7465 (t) REVERT: C 391 LYS cc_start: 0.7321 (tmtt) cc_final: 0.6491 (ttmm) REVERT: C 441 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.2420 (mt) REVERT: D 489 MET cc_start: 0.8580 (mtm) cc_final: 0.7988 (mtt) REVERT: D 498 GLU cc_start: 0.8808 (pt0) cc_final: 0.8325 (pm20) REVERT: E 391 LYS cc_start: 0.7649 (tptp) cc_final: 0.7174 (ttpt) REVERT: E 449 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (mm) REVERT: E 514 ARG cc_start: 0.8429 (mtt90) cc_final: 0.8119 (mtp85) REVERT: E 554 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7332 (tptp) REVERT: F 449 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7886 (pp) REVERT: F 453 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7532 (p0) REVERT: F 461 ARG cc_start: 0.7956 (mpp80) cc_final: 0.7569 (mtt180) REVERT: G 364 LYS cc_start: 0.7861 (tptt) cc_final: 0.7660 (tptt) REVERT: G 443 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7572 (ptm-80) REVERT: G 445 LYS cc_start: 0.7977 (tptt) cc_final: 0.7525 (pttt) REVERT: G 514 ARG cc_start: 0.6463 (mtt180) cc_final: 0.6218 (mtt180) REVERT: H 380 ILE cc_start: 0.1412 (mm) cc_final: 0.1055 (tt) REVERT: H 418 TRP cc_start: 0.7230 (t60) cc_final: 0.6902 (t60) REVERT: H 453 ASP cc_start: 0.8052 (t0) cc_final: 0.7715 (t0) REVERT: K 418 TRP cc_start: 0.6547 (OUTLIER) cc_final: 0.3965 (t-100) REVERT: K 451 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.8192 (ptp-170) REVERT: K 463 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7493 (tm-30) REVERT: K 514 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7215 (mmm-85) REVERT: L 450 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5780 (m90) REVERT: L 451 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7656 (ttm170) REVERT: L 518 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6685 (t-170) REVERT: L 561 LEU cc_start: 0.8796 (tt) cc_final: 0.8315 (pp) REVERT: L 570 ASP cc_start: 0.8377 (t0) cc_final: 0.8067 (t0) REVERT: R 90 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7403 (tm-30) REVERT: R 109 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7410 (t0) REVERT: R 112 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7201 (ptm160) outliers start: 106 outliers final: 73 residues processed: 326 average time/residue: 0.1800 time to fit residues: 83.7543 Evaluate side-chains 330 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 243 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 TRP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 156 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 40.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 545 ASN D 518 HIS E 450 HIS ** K 430 HIS ** 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 = 0.4529 r_free = 0.4529 target = 0.203315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123138 restraints weight = 27071.662| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.80 r_work: 0.3377 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19841 Z= 0.116 Angle : 0.628 12.476 27182 Z= 0.307 Chirality : 0.046 0.372 3221 Planarity : 0.005 0.058 3456 Dihedral : 7.265 59.519 2946 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.00 % Favored : 91.96 % Rotamer: Outliers : 4.63 % Allowed : 18.44 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2438 helix: -1.88 (0.35), residues: 164 sheet: -0.35 (0.17), residues: 889 loop : -1.78 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 423 TYR 0.016 0.001 TYR K 534 PHE 0.021 0.001 PHE E 424 TRP 0.020 0.001 TRP B 382 HIS 0.003 0.001 HIS L 518 Details of bonding type rmsd covalent geometry : bond 0.00267 (19802) covalent geometry : angle 0.60041 (27093) SS BOND : bond 0.00348 ( 28) SS BOND : angle 1.25324 ( 56) hydrogen bonds : bond 0.03084 ( 532) hydrogen bonds : angle 5.36982 ( 1494) link_NAG-ASN : bond 0.00847 ( 11) link_NAG-ASN : angle 5.12787 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 250 time to evaluate : 0.697 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: A 537 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8820 (m) REVERT: B 461 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7330 (tpp-160) REVERT: B 466 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6671 (pp) REVERT: B 489 MET cc_start: 0.8279 (mtt) cc_final: 0.7921 (mtp) REVERT: B 490 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: B 510 GLN cc_start: 0.8336 (pp30) cc_final: 0.8135 (pp30) REVERT: C 391 LYS cc_start: 0.7349 (tmtt) cc_final: 0.6479 (ttmm) REVERT: C 441 ILE cc_start: 0.3528 (OUTLIER) cc_final: 0.2286 (mt) REVERT: C 554 LYS cc_start: 0.7100 (tmtt) cc_final: 0.6869 (tmtt) REVERT: D 439 GLN cc_start: 0.5240 (tp40) cc_final: 0.4706 (tm-30) REVERT: D 489 MET cc_start: 0.8560 (mtm) cc_final: 0.8002 (mtt) REVERT: D 498 GLU cc_start: 0.8807 (pt0) cc_final: 0.8327 (pm20) REVERT: E 391 LYS cc_start: 0.7636 (tptp) cc_final: 0.7296 (pttt) REVERT: E 514 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8069 (mtp85) REVERT: E 554 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7352 (tptp) REVERT: F 449 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7881 (pp) REVERT: F 453 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7531 (p0) REVERT: F 461 ARG cc_start: 0.7936 (mpp80) cc_final: 0.7539 (mtt180) REVERT: F 561 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7638 (tt) REVERT: G 364 LYS cc_start: 0.7875 (tptt) cc_final: 0.7525 (tppt) REVERT: G 445 LYS cc_start: 0.7911 (tptt) cc_final: 0.7428 (pttt) REVERT: H 380 ILE cc_start: 0.1471 (mm) cc_final: 0.0943 (tt) REVERT: H 443 ARG cc_start: 0.6206 (mmp80) cc_final: 0.5990 (mmp80) REVERT: H 453 ASP cc_start: 0.8021 (t0) cc_final: 0.7668 (t0) REVERT: K 418 TRP cc_start: 0.6474 (OUTLIER) cc_final: 0.3720 (t-100) REVERT: K 451 ARG cc_start: 0.8536 (ptm-80) cc_final: 0.8174 (ptp-170) REVERT: K 463 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7500 (tm-30) REVERT: K 514 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7161 (mmm-85) REVERT: L 450 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.5804 (m90) REVERT: L 451 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7723 (ttm170) REVERT: L 561 LEU cc_start: 0.8829 (tt) cc_final: 0.8396 (pp) REVERT: L 570 ASP cc_start: 0.8337 (t0) cc_final: 0.8010 (t0) REVERT: R 109 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7323 (t0) REVERT: R 112 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7261 (ptm160) outliers start: 102 outliers final: 72 residues processed: 321 average time/residue: 0.1589 time to fit residues: 73.3060 Evaluate side-chains 317 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 234 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR 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 H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 122 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 195 optimal weight: 40.0000 chunk 88 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN E 487 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.198191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116644 restraints weight = 27288.529| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.78 r_work: 0.3286 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19841 Z= 0.276 Angle : 0.749 14.027 27182 Z= 0.371 Chirality : 0.051 0.422 3221 Planarity : 0.005 0.062 3456 Dihedral : 7.262 59.911 2926 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.01 % Favored : 89.91 % Rotamer: Outliers : 4.90 % Allowed : 18.66 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.17), residues: 2438 helix: -1.72 (0.36), residues: 158 sheet: -0.52 (0.17), residues: 899 loop : -1.90 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 443 TYR 0.016 0.002 TYR G 534 PHE 0.022 0.002 PHE G 479 TRP 0.026 0.002 TRP B 382 HIS 0.007 0.001 HIS K 518 Details of bonding type rmsd covalent geometry : bond 0.00660 (19802) covalent geometry : angle 0.71838 (27093) SS BOND : bond 0.00480 ( 28) SS BOND : angle 2.09451 ( 56) hydrogen bonds : bond 0.03722 ( 532) hydrogen bonds : angle 5.71365 ( 1494) link_NAG-ASN : bond 0.00856 ( 11) link_NAG-ASN : angle 5.50855 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 243 time to evaluate : 0.554 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: A 525 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 529 ASN cc_start: 0.8606 (m-40) cc_final: 0.8317 (p0) REVERT: A 537 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8868 (m) REVERT: B 461 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7497 (tpp-160) REVERT: B 489 MET cc_start: 0.8582 (mtt) cc_final: 0.8153 (mtt) REVERT: B 490 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: B 510 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8084 (pp30) REVERT: C 441 ILE cc_start: 0.3627 (OUTLIER) cc_final: 0.2358 (mt) REVERT: D 424 PHE cc_start: 0.8211 (m-80) cc_final: 0.7789 (m-80) REVERT: D 439 GLN cc_start: 0.5289 (tp40) cc_final: 0.4765 (tm-30) REVERT: D 453 ASP cc_start: 0.8548 (m-30) cc_final: 0.8243 (m-30) REVERT: D 489 MET cc_start: 0.8671 (mtm) cc_final: 0.8085 (mtt) REVERT: E 391 LYS cc_start: 0.7711 (tptp) cc_final: 0.7356 (pttt) REVERT: F 449 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7923 (pp) REVERT: F 453 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7654 (p0) REVERT: F 461 ARG cc_start: 0.8092 (mpp80) cc_final: 0.7714 (mtt180) REVERT: G 364 LYS cc_start: 0.7766 (tptt) cc_final: 0.7390 (tppt) REVERT: G 443 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7567 (ptm-80) REVERT: G 445 LYS cc_start: 0.7957 (tptt) cc_final: 0.7540 (pttt) REVERT: H 380 ILE cc_start: 0.1602 (mm) cc_final: 0.1065 (tt) REVERT: H 453 ASP cc_start: 0.8118 (t0) cc_final: 0.7737 (t70) REVERT: K 418 TRP cc_start: 0.6489 (OUTLIER) cc_final: 0.3592 (t-100) REVERT: K 451 ARG cc_start: 0.8501 (ptm-80) cc_final: 0.8150 (ptp-170) REVERT: K 463 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7385 (tm-30) REVERT: K 514 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7267 (mmm-85) REVERT: L 450 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5736 (m90) REVERT: L 451 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7814 (ttm170) REVERT: L 561 LEU cc_start: 0.8804 (tt) cc_final: 0.8212 (pp) REVERT: L 570 ASP cc_start: 0.8343 (t0) cc_final: 0.8067 (t0) REVERT: R 109 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7636 (t0) REVERT: R 112 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7248 (ptm160) outliers start: 108 outliers final: 78 residues processed: 319 average time/residue: 0.1531 time to fit residues: 70.1833 Evaluate side-chains 317 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 228 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 TRP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR 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 H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 71 optimal weight: 0.0270 chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 190 optimal weight: 40.0000 chunk 143 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 393 HIS ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 518 HIS ** R 121 ASN ** 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 = 0.4523 r_free = 0.4523 target = 0.202675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122690 restraints weight = 27191.200| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.75 r_work: 0.3378 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19841 Z= 0.116 Angle : 0.652 12.855 27182 Z= 0.318 Chirality : 0.046 0.356 3221 Planarity : 0.005 0.064 3456 Dihedral : 6.682 58.315 2922 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.00 % Favored : 91.96 % Rotamer: Outliers : 4.36 % Allowed : 19.62 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2438 helix: -1.61 (0.37), residues: 157 sheet: -0.31 (0.17), residues: 893 loop : -1.65 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.015 0.001 TYR K 534 PHE 0.017 0.001 PHE L 516 TRP 0.033 0.001 TRP B 382 HIS 0.007 0.001 HIS G 430 Details of bonding type rmsd covalent geometry : bond 0.00266 (19802) covalent geometry : angle 0.62399 (27093) SS BOND : bond 0.00409 ( 28) SS BOND : angle 1.50825 ( 56) hydrogen bonds : bond 0.03062 ( 532) hydrogen bonds : angle 5.32871 ( 1494) link_NAG-ASN : bond 0.00857 ( 11) link_NAG-ASN : angle 5.13757 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 248 time to evaluate : 0.725 Fit side-chains 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: A 455 TYR cc_start: 0.8377 (m-80) cc_final: 0.8174 (m-80) REVERT: B 461 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7274 (tpp-160) REVERT: B 466 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6714 (pp) REVERT: B 489 MET cc_start: 0.8333 (mtt) cc_final: 0.7932 (mtp) REVERT: B 490 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: B 510 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8278 (pp30) REVERT: C 371 ASP cc_start: 0.6462 (t70) cc_final: 0.6120 (m-30) REVERT: C 391 LYS cc_start: 0.7345 (tmtt) cc_final: 0.6492 (ttmm) REVERT: C 441 ILE cc_start: 0.3602 (OUTLIER) cc_final: 0.2400 (mt) REVERT: C 489 MET cc_start: 0.8649 (mtt) cc_final: 0.8394 (mtt) REVERT: D 414 CYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6380 (m) REVERT: D 439 GLN cc_start: 0.5373 (tp40) cc_final: 0.4893 (tm-30) REVERT: D 489 MET cc_start: 0.8634 (mtm) cc_final: 0.8079 (mtt) REVERT: D 498 GLU cc_start: 0.8813 (pt0) cc_final: 0.8324 (pm20) REVERT: E 391 LYS cc_start: 0.7679 (tptp) cc_final: 0.7390 (pttt) REVERT: E 500 TYR cc_start: 0.8967 (p90) cc_final: 0.8757 (p90) REVERT: E 514 ARG cc_start: 0.8540 (mpt-90) cc_final: 0.8261 (mtt-85) REVERT: E 554 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7335 (tptp) REVERT: F 449 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7929 (pp) REVERT: F 453 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7510 (p0) REVERT: F 461 ARG cc_start: 0.7986 (mpp80) cc_final: 0.7654 (mtt180) REVERT: G 441 ILE cc_start: 0.4549 (OUTLIER) cc_final: 0.4244 (pt) REVERT: H 380 ILE cc_start: 0.1407 (mm) cc_final: 0.0854 (tt) REVERT: H 453 ASP cc_start: 0.8019 (t0) cc_final: 0.7708 (t70) REVERT: H 461 ARG cc_start: 0.8499 (mtm110) cc_final: 0.8297 (mmt90) REVERT: K 451 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8169 (ptp-170) REVERT: K 463 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7374 (tm-30) REVERT: K 514 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7133 (mmm-85) REVERT: L 450 HIS cc_start: 0.6169 (OUTLIER) cc_final: 0.5827 (m90) REVERT: L 451 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7760 (ttm170) REVERT: L 561 LEU cc_start: 0.8804 (tt) cc_final: 0.8430 (pp) REVERT: L 570 ASP cc_start: 0.8284 (t0) cc_final: 0.8009 (t0) REVERT: R 109 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7457 (t0) REVERT: R 112 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7166 (ptm160) outliers start: 96 outliers final: 69 residues processed: 315 average time/residue: 0.1611 time to fit residues: 73.2447 Evaluate side-chains 318 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 238 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR 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 H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 192 optimal weight: 0.0370 chunk 133 optimal weight: 8.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 439 GLN G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 121 ASN ** 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 = 0.4498 r_free = 0.4498 target = 0.200107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119228 restraints weight = 27112.798| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.80 r_work: 0.3323 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19841 Z= 0.192 Angle : 0.685 13.633 27182 Z= 0.338 Chirality : 0.048 0.399 3221 Planarity : 0.005 0.062 3456 Dihedral : 6.656 59.760 2917 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 4.18 % Allowed : 19.89 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.17), residues: 2438 helix: -1.48 (0.38), residues: 163 sheet: -0.35 (0.17), residues: 891 loop : -1.73 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 514 TYR 0.013 0.001 TYR K 534 PHE 0.022 0.002 PHE E 424 TRP 0.038 0.001 TRP B 382 HIS 0.006 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00460 (19802) covalent geometry : angle 0.65772 (27093) SS BOND : bond 0.00434 ( 28) SS BOND : angle 1.58221 ( 56) hydrogen bonds : bond 0.03267 ( 532) hydrogen bonds : angle 5.38751 ( 1494) link_NAG-ASN : bond 0.00808 ( 11) link_NAG-ASN : angle 5.23407 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 233 time to evaluate : 0.543 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: A 537 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8849 (m) REVERT: B 461 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7423 (tpp-160) REVERT: B 489 MET cc_start: 0.8389 (mtt) cc_final: 0.8067 (mtp) REVERT: B 490 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 371 ASP cc_start: 0.6519 (t70) cc_final: 0.6169 (m-30) REVERT: C 441 ILE cc_start: 0.3698 (OUTLIER) cc_final: 0.2475 (mt) REVERT: D 414 CYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6360 (m) REVERT: D 489 MET cc_start: 0.8671 (mtm) cc_final: 0.8103 (mtt) REVERT: E 391 LYS cc_start: 0.7700 (tptp) cc_final: 0.7403 (pttt) REVERT: F 449 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7986 (pp) REVERT: F 453 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7561 (p0) REVERT: G 364 LYS cc_start: 0.7677 (tptt) cc_final: 0.7275 (tppt) REVERT: G 441 ILE cc_start: 0.4592 (OUTLIER) cc_final: 0.4277 (pt) REVERT: G 443 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7631 (ptm-80) REVERT: G 445 LYS cc_start: 0.7858 (tptm) cc_final: 0.7505 (pttt) REVERT: H 380 ILE cc_start: 0.1614 (mm) cc_final: 0.1074 (tt) REVERT: H 453 ASP cc_start: 0.8044 (t0) cc_final: 0.7698 (t70) REVERT: H 461 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8386 (mmt90) REVERT: K 451 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.8143 (ptp-170) REVERT: K 463 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7362 (tm-30) REVERT: K 467 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7762 (tpp80) REVERT: K 514 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7250 (mmm-85) REVERT: L 450 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5735 (m90) REVERT: L 451 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7884 (ttm170) REVERT: L 561 LEU cc_start: 0.8830 (tt) cc_final: 0.8351 (pp) REVERT: L 570 ASP cc_start: 0.8312 (t0) cc_final: 0.8052 (t0) REVERT: R 109 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7625 (t0) REVERT: R 112 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7214 (ptm160) outliers start: 92 outliers final: 73 residues processed: 301 average time/residue: 0.1532 time to fit residues: 67.0297 Evaluate side-chains 313 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 229 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR 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 H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 464 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 74 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 83 optimal weight: 0.0020 chunk 200 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 121 ASN ** 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 = 0.4517 r_free = 0.4517 target = 0.202069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121758 restraints weight = 27295.527| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.77 r_work: 0.3358 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19841 Z= 0.131 Angle : 0.657 13.293 27182 Z= 0.322 Chirality : 0.047 0.376 3221 Planarity : 0.005 0.060 3456 Dihedral : 6.443 59.418 2917 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % Rotamer: Outliers : 3.91 % Allowed : 20.03 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2438 helix: -1.42 (0.39), residues: 157 sheet: -0.25 (0.17), residues: 895 loop : -1.58 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 514 TYR 0.014 0.001 TYR K 534 PHE 0.022 0.001 PHE E 424 TRP 0.036 0.001 TRP B 382 HIS 0.005 0.001 HIS G 430 Details of bonding type rmsd covalent geometry : bond 0.00310 (19802) covalent geometry : angle 0.63057 (27093) SS BOND : bond 0.00377 ( 28) SS BOND : angle 1.38133 ( 56) hydrogen bonds : bond 0.03030 ( 532) hydrogen bonds : angle 5.19457 ( 1494) link_NAG-ASN : bond 0.00815 ( 11) link_NAG-ASN : angle 5.08336 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 0.682 Fit side-chains 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: A 537 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8849 (m) REVERT: B 461 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7379 (tpp-160) REVERT: B 489 MET cc_start: 0.8298 (mtt) cc_final: 0.7934 (mtp) REVERT: C 371 ASP cc_start: 0.6521 (t70) cc_final: 0.6177 (m-30) REVERT: C 391 LYS cc_start: 0.7447 (tmtt) cc_final: 0.6617 (ttmm) REVERT: C 393 HIS cc_start: 0.3638 (OUTLIER) cc_final: 0.3361 (m90) REVERT: C 441 ILE cc_start: 0.3712 (OUTLIER) cc_final: 0.2498 (mt) REVERT: C 489 MET cc_start: 0.8671 (mtt) cc_final: 0.8453 (mtt) REVERT: D 414 CYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6361 (m) REVERT: D 489 MET cc_start: 0.8660 (mtm) cc_final: 0.8108 (mtt) REVERT: D 498 GLU cc_start: 0.8829 (pt0) cc_final: 0.8339 (pm20) REVERT: E 391 LYS cc_start: 0.7667 (tptp) cc_final: 0.7380 (pttt) REVERT: E 500 TYR cc_start: 0.9027 (p90) cc_final: 0.8738 (p90) REVERT: E 554 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7364 (tptp) REVERT: F 449 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7972 (pp) REVERT: F 453 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7527 (p0) REVERT: F 461 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7677 (mtt180) REVERT: F 462 GLU cc_start: 0.8490 (mp0) cc_final: 0.8246 (mt-10) REVERT: G 441 ILE cc_start: 0.4545 (OUTLIER) cc_final: 0.4307 (pt) REVERT: G 443 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7502 (ptm-80) REVERT: G 445 LYS cc_start: 0.7786 (tptm) cc_final: 0.7454 (pttt) REVERT: H 380 ILE cc_start: 0.1547 (mm) cc_final: 0.1031 (tt) REVERT: H 453 ASP cc_start: 0.8037 (t0) cc_final: 0.7727 (t70) REVERT: H 461 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8373 (mmt90) REVERT: K 451 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.8238 (ptp90) REVERT: K 463 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7319 (tm-30) REVERT: K 514 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7187 (mmm-85) REVERT: L 450 HIS cc_start: 0.6124 (OUTLIER) cc_final: 0.5810 (m90) REVERT: L 561 LEU cc_start: 0.8805 (tt) cc_final: 0.8469 (pp) REVERT: L 570 ASP cc_start: 0.8265 (t0) cc_final: 0.8019 (t0) REVERT: R 109 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7607 (t0) REVERT: R 112 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7214 (ptm160) outliers start: 86 outliers final: 68 residues processed: 306 average time/residue: 0.1672 time to fit residues: 74.0440 Evaluate side-chains 312 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR 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 H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 40 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 40.0000 chunk 138 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** 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 = 0.4505 r_free = 0.4505 target = 0.200961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120463 restraints weight = 27209.939| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.76 r_work: 0.3342 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19841 Z= 0.164 Angle : 0.672 13.549 27182 Z= 0.331 Chirality : 0.048 0.390 3221 Planarity : 0.005 0.058 3456 Dihedral : 6.372 59.845 2912 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.06 % Favored : 90.89 % Rotamer: Outliers : 4.18 % Allowed : 20.12 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.17), residues: 2438 helix: -1.42 (0.39), residues: 157 sheet: -0.22 (0.17), residues: 894 loop : -1.60 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 514 TYR 0.013 0.001 TYR D 534 PHE 0.022 0.002 PHE L 516 TRP 0.042 0.001 TRP B 382 HIS 0.005 0.001 HIS G 430 Details of bonding type rmsd covalent geometry : bond 0.00392 (19802) covalent geometry : angle 0.64548 (27093) SS BOND : bond 0.00405 ( 28) SS BOND : angle 1.42561 ( 56) hydrogen bonds : bond 0.03167 ( 532) hydrogen bonds : angle 5.19323 ( 1494) link_NAG-ASN : bond 0.00796 ( 11) link_NAG-ASN : angle 5.13399 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6378.92 seconds wall clock time: 109 minutes 47.38 seconds (6587.38 seconds total)