Starting phenix.real_space_refine on Sat Jul 4 07:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytc_34085/07_2026/7ytc_34085.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.76, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 798.1 milliseconds 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: 0.67 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: 3.37 Time building geometry restraints manager: 2.24 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 - 17.93: 10518 17.93 - 35.85: 1029 35.85 - 53.78: 318 53.78 - 71.70: 79 71.70 - 89.63: 21 Dihedral angle restraints: 11965 sinusoidal: 4718 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 11962 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 16.461 89.627 7157 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 are 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/Z covalent geometry : bond 0.01066 / 0.73 (19802) covalent geometry : angle 1.32177 / 0.83 (27093) SS BOND : bond 0.00836 / 0.57 ( 28) SS BOND : angle 2.24040 / 1.33 ( 56) hydrogen bonds : bond 0.19892 / 13.23 ( 532) hydrogen bonds : angle 8.25738 / 5.90 ( 1494) link_NAG-ASN : bond 0.08924 / 3.11 ( 11) link_NAG-ASN : angle 12.82384 / 8.07 ( 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 : 0.763 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: 0.8630 (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: 0.1771 time to fit residues: 118.2423 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 : 0.791 ------------------------------------------------------------------------------- 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... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 439 GLN C 450 HIS ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.204986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125104 restraints weight = 27282.894| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.83 r_work: 0.3408 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19841 Z= 0.151 Angle : 0.718 12.829 27182 Z= 0.361 Chirality : 0.050 0.392 3221 Planarity : 0.006 0.084 3456 Dihedral : 10.158 84.361 2879 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 4.81 % Allowed : 10.94 % Favored : 84.24 % 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 are not related in a simple way. whole: -2.32 (0.16), residues: 2438 helix: -2.40 (0.33), 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 0.007 0.001 ARG A 443 TYR 0.028 0.002 TYR C 534 PHE 0.026 0.002 PHE B 348 TRP 0.028 0.002 TRP H 382 HIS 0.007 0.001 HIS E 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (19802) covalent geometry : angle 0.69529 / 0.36 (27093) SS BOND : bond 0.00553 / 0.34 ( 28) SS BOND : angle 1.12562 / 0.66 ( 56) hydrogen bonds : bond 0.04095 / 2.75 ( 532) hydrogen bonds : angle 6.39947 / 4.47 ( 1494) link_NAG-ASN : bond 0.01120 / 0.65 ( 11) link_NAG-ASN : angle 5.02481 / 3.46 ( 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 390 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 284 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7510 (pptt) REVERT: B 461 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7281 (tpp-160) REVERT: B 499 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: B 510 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: B 546 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7681 (ttm170) REVERT: D 489 MET cc_start: 0.8209 (mtm) cc_final: 0.7757 (mtt) REVERT: E 453 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6997 (p0) REVERT: E 500 TYR cc_start: 0.9063 (p90) cc_final: 0.8758 (p90) REVERT: E 554 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7475 (tmtt) REVERT: F 449 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7834 (pp) REVERT: F 453 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7286 (p0) REVERT: F 461 ARG cc_start: 0.7769 (mpp80) cc_final: 0.7298 (mtt180) REVERT: G 364 LYS cc_start: 0.7816 (tptt) cc_final: 0.7466 (tppt) REVERT: G 443 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7733 (ptm-80) REVERT: J 9 ASP cc_start: 0.8224 (t70) cc_final: 0.7768 (t70) REVERT: J 16 ARG cc_start: 0.8119 (tmt170) cc_final: 0.7350 (tmt170) REVERT: J 106 ASN cc_start: 0.7771 (p0) cc_final: 0.7420 (m-40) REVERT: K 451 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8194 (ptm-80) REVERT: K 530 THR cc_start: 0.7050 (OUTLIER) cc_final: 0.6493 (t) REVERT: K 554 LYS cc_start: 0.8375 (tttt) cc_final: 0.7980 (tttm) REVERT: L 450 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5714 (m90) REVERT: L 451 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7621 (ttm170) REVERT: L 518 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6631 (t-170) REVERT: R 109 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7642 (t0) REVERT: R 121 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6901 (t0) outliers start: 106 outliers final: 59 residues processed: 358 average time/residue: 0.1760 time to fit residues: 91.2417 Evaluate side-chains 312 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 491 ARG Chi-restraints excluded: chain B residue 499 LYS 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 553 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 447 VAL 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 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 451 ARG 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 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 39 LEU 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: 0.7980 chunk 109 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN B 419 ASN B 510 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 = 0.4526 r_free = 0.4526 target = 0.203031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122513 restraints weight = 27356.053| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.81 r_work: 0.3377 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19841 Z= 0.158 Angle : 0.673 12.650 27182 Z= 0.335 Chirality : 0.048 0.372 3221 Planarity : 0.005 0.070 3456 Dihedral : 8.142 74.611 2755 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.49 % Favored : 91.43 % Rotamer: Outliers : 3.68 % Allowed : 15.26 % Favored : 81.06 % 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 are not related in a simple way. whole: -2.20 (0.16), residues: 2438 helix: -2.23 (0.34), residues: 166 sheet: -0.60 (0.17), residues: 891 loop : -2.00 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.019 0.001 TYR K 534 PHE 0.020 0.002 PHE B 348 TRP 0.015 0.001 TRP B 418 HIS 0.004 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (19802) covalent geometry : angle 0.65032 / 0.33 (27093) SS BOND : bond 0.00434 / 0.27 ( 28) SS BOND : angle 1.25056 / 0.76 ( 56) hydrogen bonds : bond 0.03593 / 2.40 ( 532) hydrogen bonds : angle 5.89508 / 4.11 ( 1494) link_NAG-ASN : bond 0.00898 / 0.61 ( 11) link_NAG-ASN : angle 4.82987 / 3.41 ( 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 349 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7742 (pptt) REVERT: B 461 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7396 (tpp-160) REVERT: B 489 MET cc_start: 0.8402 (mtt) cc_final: 0.7649 (mtt) REVERT: B 490 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: B 491 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.6224 (mpt-90) REVERT: B 510 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8222 (pp30) REVERT: B 533 THR cc_start: 0.7886 (m) cc_final: 0.7589 (t) REVERT: B 534 TYR cc_start: 0.8410 (m-80) cc_final: 0.8193 (m-80) REVERT: D 489 MET cc_start: 0.8424 (mtm) cc_final: 0.7890 (mtt) REVERT: E 391 LYS cc_start: 0.7665 (tptp) cc_final: 0.7106 (ttpt) REVERT: E 440 THR cc_start: 0.5227 (OUTLIER) cc_final: 0.4803 (p) REVERT: E 449 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8458 (mm) REVERT: E 453 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7056 (p0) REVERT: E 554 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7554 (tmtt) REVERT: F 449 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7856 (pp) REVERT: F 453 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7688 (p0) REVERT: H 568 MET cc_start: 0.7272 (mmm) cc_final: 0.6902 (mmm) REVERT: J 106 ASN cc_start: 0.7817 (p0) cc_final: 0.7566 (m-40) REVERT: K 418 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.5502 (m-90) REVERT: K 514 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.6964 (mtp85) REVERT: L 450 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.5762 (m90) REVERT: L 451 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: L 518 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6589 (t-170) REVERT: R 109 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7479 (t0) outliers start: 81 outliers final: 52 residues processed: 323 average time/residue: 0.1689 time to fit residues: 79.2388 Evaluate side-chains 306 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 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 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 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 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 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 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 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 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 H residue 566 LEU 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 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 518 HIS Chi-restraints excluded: chain R residue 33 VAL 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 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: 40.0000 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 40.0000 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 439 GLN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 = 0.4508 r_free = 0.4508 target = 0.201060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120006 restraints weight = 27430.749| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.83 r_work: 0.3337 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19841 Z= 0.192 Angle : 0.676 13.144 27182 Z= 0.337 Chirality : 0.049 0.374 3221 Planarity : 0.005 0.072 3456 Dihedral : 7.410 71.543 2720 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.02 % Favored : 90.89 % Rotamer: Outliers : 4.77 % Allowed : 16.58 % 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 are not related in a simple way. whole: -2.17 (0.16), residues: 2438 helix: -2.20 (0.34), residues: 171 sheet: -0.57 (0.17), residues: 876 loop : -1.98 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 461 TYR 0.018 0.001 TYR K 534 PHE 0.018 0.002 PHE B 479 TRP 0.016 0.001 TRP H 418 HIS 0.005 0.001 HIS H 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (19802) covalent geometry : angle 0.65217 / 0.33 (27093) SS BOND : bond 0.00431 / 0.26 ( 28) SS BOND : angle 1.32007 / 0.82 ( 56) hydrogen bonds : bond 0.03494 / 2.35 ( 532) hydrogen bonds : angle 5.75475 / 4.00 ( 1494) link_NAG-ASN : bond 0.00848 / 0.58 ( 11) link_NAG-ASN : angle 4.89258 / 3.42 ( 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 355 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 250 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7837 (pptt) REVERT: B 461 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7395 (tpp-160) REVERT: B 489 MET cc_start: 0.8464 (mtt) cc_final: 0.8222 (mtt) REVERT: B 490 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: B 491 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6216 (mpt-90) REVERT: B 533 THR cc_start: 0.7842 (m) cc_final: 0.7560 (t) REVERT: C 469 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7785 (p) REVERT: D 489 MET cc_start: 0.8522 (mtm) cc_final: 0.7928 (mtt) REVERT: E 391 LYS cc_start: 0.7639 (tptp) cc_final: 0.7100 (ttpt) REVERT: E 440 THR cc_start: 0.5298 (OUTLIER) cc_final: 0.4524 (p) REVERT: E 449 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8433 (mm) REVERT: E 554 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7359 (tptp) REVERT: F 449 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7889 (pp) REVERT: F 453 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7603 (p0) REVERT: F 461 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7543 (mtt180) REVERT: G 443 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7334 (ptm-80) REVERT: G 445 LYS cc_start: 0.7946 (tptt) cc_final: 0.7520 (pttt) REVERT: H 453 ASP cc_start: 0.7907 (t0) cc_final: 0.7705 (t0) REVERT: J 9 ASP cc_start: 0.8410 (t70) cc_final: 0.8206 (t0) REVERT: K 418 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.4220 (t-100) REVERT: K 514 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.6934 (mtp85) REVERT: L 450 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5784 (m90) REVERT: L 451 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7730 (ttm170) REVERT: L 514 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.4817 (ptp90) REVERT: L 518 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6691 (t-170) REVERT: R 75 ARG cc_start: 0.6300 (ptp90) cc_final: 0.5995 (ptt180) REVERT: R 90 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7467 (tm-30) REVERT: R 109 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7313 (t0) REVERT: R 112 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7255 (ptm160) outliers start: 105 outliers final: 69 residues processed: 322 average time/residue: 0.1592 time to fit residues: 74.8713 Evaluate side-chains 316 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 232 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 357 ILE Chi-restraints excluded: chain B residue 414 CYS 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 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 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 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 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 363 THR Chi-restraints excluded: chain H residue 414 CYS 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 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 49 ILE 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 514 ARG Chi-restraints excluded: chain L residue 518 HIS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 235 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 232 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 126 optimal weight: 0.0770 chunk 23 optimal weight: 40.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 463 GLN D 518 HIS ** 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 = 0.4537 r_free = 0.4537 target = 0.204141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.123881 restraints weight = 27189.025| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.82 r_work: 0.3382 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19841 Z= 0.113 Angle : 0.619 12.077 27182 Z= 0.306 Chirality : 0.046 0.341 3221 Planarity : 0.005 0.062 3456 Dihedral : 6.956 58.424 2720 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 4.41 % Allowed : 17.03 % Favored : 78.56 % 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 are not related in a simple way. whole: -1.90 (0.17), residues: 2438 helix: -1.92 (0.35), residues: 164 sheet: -0.40 (0.17), residues: 882 loop : -1.79 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 50 TYR 0.018 0.001 TYR K 534 PHE 0.012 0.001 PHE B 348 TRP 0.014 0.001 TRP B 382 HIS 0.004 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19802) covalent geometry : angle 0.59519 / 0.30 (27093) SS BOND : bond 0.00395 / 0.26 ( 28) SS BOND : angle 1.46109 / 0.97 ( 56) hydrogen bonds : bond 0.03134 / 2.10 ( 532) hydrogen bonds : angle 5.40144 / 3.75 ( 1494) link_NAG-ASN : bond 0.00829 / 0.56 ( 11) link_NAG-ASN : angle 4.62387 / 3.32 ( 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 356 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 259 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8786 (m) REVERT: B 445 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7920 (pptt) REVERT: B 461 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7328 (tpp-160) REVERT: B 490 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 514 ARG cc_start: 0.7476 (mtp-110) cc_final: 0.7144 (mtp-110) REVERT: B 533 THR cc_start: 0.7703 (m) cc_final: 0.7444 (t) REVERT: B 534 TYR cc_start: 0.8412 (m-80) cc_final: 0.8112 (m-80) REVERT: D 489 MET cc_start: 0.8522 (mtm) cc_final: 0.7938 (mtt) REVERT: D 498 GLU cc_start: 0.8809 (pt0) cc_final: 0.8334 (pm20) REVERT: E 391 LYS cc_start: 0.7597 (tptp) cc_final: 0.7135 (ttpt) REVERT: E 449 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8372 (mm) REVERT: F 449 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7854 (pp) REVERT: F 453 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7485 (p0) REVERT: F 461 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7647 (mtt180) REVERT: F 489 MET cc_start: 0.7262 (mmt) cc_final: 0.7006 (mmt) REVERT: G 364 LYS cc_start: 0.7835 (tptt) cc_final: 0.7525 (tppt) REVERT: G 443 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7704 (ptm-80) REVERT: G 445 LYS cc_start: 0.7974 (tptt) cc_final: 0.7518 (pttt) REVERT: H 380 ILE cc_start: 0.1503 (mm) cc_final: 0.0969 (tt) REVERT: H 453 ASP cc_start: 0.7869 (t0) cc_final: 0.7618 (t0) REVERT: K 418 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.3955 (t-100) REVERT: K 463 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7777 (tm-30) REVERT: K 514 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7229 (mmm-85) REVERT: L 450 HIS cc_start: 0.6135 (OUTLIER) cc_final: 0.5774 (m90) REVERT: L 451 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7628 (ttm170) REVERT: L 561 LEU cc_start: 0.8765 (tt) cc_final: 0.8316 (pp) REVERT: R 109 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7212 (t0) REVERT: R 112 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7148 (ptm160) outliers start: 97 outliers final: 62 residues processed: 323 average time/residue: 0.1621 time to fit residues: 76.4275 Evaluate side-chains 314 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 241 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 TRP 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 413 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 535 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 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 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 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 538 VAL 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 522 THR 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 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 414 CYS 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 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 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 552 VAL 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: 2.9990 chunk 59 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 545 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.201722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121284 restraints weight = 27151.484| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.75 r_work: 0.3354 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2954 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= 0.170 Angle : 0.654 12.717 27182 Z= 0.324 Chirality : 0.048 0.365 3221 Planarity : 0.005 0.062 3456 Dihedral : 6.764 59.366 2711 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.45 % Allowed : 18.80 % Favored : 76.75 % 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 are not related in a simple way. whole: -1.86 (0.17), residues: 2438 helix: -1.88 (0.36), residues: 164 sheet: -0.40 (0.17), residues: 887 loop : -1.76 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 423 TYR 0.015 0.001 TYR K 534 PHE 0.024 0.002 PHE L 516 TRP 0.021 0.001 TRP B 382 HIS 0.004 0.001 HIS H 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (19802) covalent geometry : angle 0.63149 / 0.32 (27093) SS BOND : bond 0.00387 / 0.23 ( 28) SS BOND : angle 1.31614 / 0.85 ( 56) hydrogen bonds : bond 0.03244 / 2.17 ( 532) hydrogen bonds : angle 5.44187 / 3.78 ( 1494) link_NAG-ASN : bond 0.00811 / 0.55 ( 11) link_NAG-ASN : angle 4.70181 / 3.29 ( 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 341 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 243 time to evaluate : 0.792 Fit side-chains 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 455 TYR cc_start: 0.8495 (m-80) cc_final: 0.8231 (m-80) REVERT: A 537 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8829 (m) REVERT: B 461 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7405 (tpp-160) REVERT: B 490 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: B 533 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7458 (t) REVERT: D 439 GLN cc_start: 0.5231 (tp40) cc_final: 0.4690 (tm-30) REVERT: D 489 MET cc_start: 0.8606 (mtm) cc_final: 0.8024 (mtt) REVERT: D 498 GLU cc_start: 0.8824 (pt0) cc_final: 0.8340 (pm20) REVERT: E 391 LYS cc_start: 0.7625 (tptp) cc_final: 0.7290 (pttt) REVERT: E 449 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8432 (mm) REVERT: E 554 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7392 (tptp) REVERT: F 449 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7954 (pp) REVERT: F 453 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7529 (p0) REVERT: F 561 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7618 (tt) REVERT: G 445 LYS cc_start: 0.7968 (tptt) cc_final: 0.7514 (pttt) REVERT: H 380 ILE cc_start: 0.1504 (mm) cc_final: 0.0987 (tt) REVERT: H 453 ASP cc_start: 0.7853 (t0) cc_final: 0.7634 (t0) REVERT: K 418 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.3741 (t-100) REVERT: K 451 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.8142 (ptp-170) REVERT: K 463 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7529 (tm-30) REVERT: K 514 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7273 (mmm-85) REVERT: L 450 HIS cc_start: 0.6078 (OUTLIER) cc_final: 0.5830 (m90) REVERT: L 451 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7733 (ttm170) REVERT: L 514 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.4809 (ptp90) REVERT: L 518 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6660 (t-170) REVERT: L 561 LEU cc_start: 0.8765 (tt) cc_final: 0.8277 (pp) REVERT: L 570 ASP cc_start: 0.8363 (t0) cc_final: 0.8091 (t0) REVERT: R 90 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7424 (tm-30) REVERT: R 109 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7405 (t0) REVERT: R 112 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7281 (ptm160) outliers start: 98 outliers final: 70 residues processed: 308 average time/residue: 0.1589 time to fit residues: 71.3822 Evaluate side-chains 316 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 233 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 490 GLN Chi-restraints excluded: chain B residue 506 MET 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 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 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 VAL 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 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 473 THR 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 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 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 514 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 122 optimal weight: 0.8980 chunk 205 optimal weight: 0.2980 chunk 224 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 199 optimal weight: 0.0370 chunk 208 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 88 optimal weight: 0.0870 chunk 177 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN R 80 GLN ** R 121 ASN ** 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 = 0.4538 r_free = 0.4538 target = 0.204282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124016 restraints weight = 27294.586| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.84 r_work: 0.3394 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3114 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= 0.111 Angle : 0.617 11.914 27182 Z= 0.304 Chirality : 0.046 0.337 3221 Planarity : 0.005 0.058 3456 Dihedral : 6.162 56.828 2697 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.18 % Allowed : 19.71 % Favored : 76.11 % 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 are not related in a simple way. whole: -1.67 (0.17), residues: 2438 helix: -1.76 (0.36), residues: 164 sheet: -0.25 (0.17), residues: 891 loop : -1.65 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 514 TYR 0.015 0.001 TYR K 534 PHE 0.023 0.001 PHE L 516 TRP 0.027 0.001 TRP H 418 HIS 0.009 0.001 HIS G 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (19802) covalent geometry : angle 0.59657 / 0.30 (27093) SS BOND : bond 0.00357 / 0.23 ( 28) SS BOND : angle 1.03253 / 0.67 ( 56) hydrogen bonds : bond 0.02987 / 2.00 ( 532) hydrogen bonds : angle 5.21485 / 3.62 ( 1494) link_NAG-ASN : bond 0.00802 / 0.54 ( 11) link_NAG-ASN : angle 4.47656 / 3.22 ( 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 348 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 256 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 ASN cc_start: 0.8634 (m-40) cc_final: 0.8353 (p0) REVERT: A 537 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8767 (m) REVERT: B 461 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7273 (tpp-160) REVERT: C 391 LYS cc_start: 0.7365 (tmtt) cc_final: 0.6559 (ttmm) REVERT: D 439 GLN cc_start: 0.5359 (tp40) cc_final: 0.4824 (tm-30) REVERT: D 489 MET cc_start: 0.8556 (mtm) cc_final: 0.7992 (mtt) REVERT: D 498 GLU cc_start: 0.8809 (pt0) cc_final: 0.8327 (pm20) REVERT: D 534 TYR cc_start: 0.8031 (m-10) cc_final: 0.7798 (m-80) REVERT: E 391 LYS cc_start: 0.7661 (tptp) cc_final: 0.7369 (pttt) REVERT: E 554 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7403 (tptp) REVERT: F 449 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7949 (pp) REVERT: F 453 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7479 (p0) REVERT: F 489 MET cc_start: 0.7247 (mmt) cc_final: 0.7023 (mmt) REVERT: F 527 GLU cc_start: 0.8322 (mp0) cc_final: 0.8090 (mp0) REVERT: F 561 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7576 (tt) REVERT: G 364 LYS cc_start: 0.7694 (tptt) cc_final: 0.7355 (tppt) REVERT: G 441 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.4203 (pt) REVERT: G 445 LYS cc_start: 0.8003 (tptt) cc_final: 0.7516 (pttt) REVERT: H 380 ILE cc_start: 0.1288 (mm) cc_final: 0.0672 (tt) REVERT: H 453 ASP cc_start: 0.7825 (t0) cc_final: 0.7504 (t0) REVERT: K 451 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8176 (ptp-170) REVERT: K 463 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7399 (tm-30) REVERT: K 514 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7153 (mmm-85) REVERT: L 450 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.5834 (m90) REVERT: L 451 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: L 493 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6526 (mp10) REVERT: L 561 LEU cc_start: 0.8765 (tt) cc_final: 0.8376 (pp) REVERT: L 570 ASP cc_start: 0.8375 (t0) cc_final: 0.8089 (t0) REVERT: R 90 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7440 (tm-30) REVERT: R 109 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7252 (t0) REVERT: R 112 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.7148 (ptm160) outliers start: 92 outliers final: 65 residues processed: 317 average time/residue: 0.1602 time to fit residues: 74.7046 Evaluate side-chains 322 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 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 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 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 447 VAL 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 E residue 453 ASP Chi-restraints excluded: chain E residue 522 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 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 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 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 451 ARG Chi-restraints excluded: chain L residue 493 GLN Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 71 optimal weight: 0.0470 chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 194 optimal weight: 20.0000 chunk 178 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 143 optimal weight: 0.0000 chunk 94 optimal weight: 20.0000 chunk 165 optimal weight: 0.4980 chunk 207 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 overall best weight: 0.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN D 493 GLN ** K 430 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.204949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125299 restraints weight = 27284.991| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.77 r_work: 0.3398 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19841 Z= 0.104 Angle : 0.621 11.671 27182 Z= 0.305 Chirality : 0.046 0.348 3221 Planarity : 0.005 0.059 3456 Dihedral : 5.878 56.418 2687 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.77 % Allowed : 19.98 % Favored : 76.25 % 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 are not related in a simple way. whole: -1.60 (0.17), residues: 2438 helix: -1.86 (0.34), residues: 176 sheet: -0.16 (0.17), residues: 893 loop : -1.60 (0.17), residues: 1369 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 0.021 0.001 PHE L 516 TRP 0.029 0.001 TRP B 382 HIS 0.005 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (19802) covalent geometry : angle 0.59764 / 0.30 (27093) SS BOND : bond 0.00405 / 0.28 ( 28) SS BOND : angle 1.75479 / 1.19 ( 56) hydrogen bonds : bond 0.02906 / 1.96 ( 532) hydrogen bonds : angle 5.11135 / 3.54 ( 1494) link_NAG-ASN : bond 0.00814 / 0.55 ( 11) link_NAG-ASN : angle 4.37104 / 3.14 ( 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 340 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 257 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8770 (m) REVERT: B 461 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7288 (tpp-160) REVERT: B 490 GLN cc_start: 0.7911 (tt0) cc_final: 0.7644 (tt0) REVERT: B 510 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7941 (pp30) REVERT: B 514 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.6860 (mtp-110) REVERT: C 391 LYS cc_start: 0.7401 (tmtt) cc_final: 0.6542 (ttmm) REVERT: C 489 MET cc_start: 0.8556 (mtt) cc_final: 0.8291 (mtt) REVERT: D 439 GLN cc_start: 0.5381 (tp40) cc_final: 0.4909 (tm-30) REVERT: D 489 MET cc_start: 0.8551 (mtm) cc_final: 0.7996 (mtt) REVERT: D 498 GLU cc_start: 0.8797 (pt0) cc_final: 0.8325 (pm20) REVERT: D 534 TYR cc_start: 0.8007 (m-10) cc_final: 0.7782 (m-80) REVERT: E 391 LYS cc_start: 0.7621 (tptp) cc_final: 0.7354 (pttt) REVERT: E 554 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7332 (tptp) REVERT: F 449 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7913 (pp) REVERT: F 453 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7471 (p0) REVERT: F 489 MET cc_start: 0.7142 (mmt) cc_final: 0.6924 (mmt) REVERT: F 527 GLU cc_start: 0.8327 (mp0) cc_final: 0.8114 (mp0) REVERT: F 561 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7496 (tt) REVERT: G 364 LYS cc_start: 0.7725 (tptt) cc_final: 0.7445 (tppt) REVERT: G 441 ILE cc_start: 0.4446 (OUTLIER) cc_final: 0.4164 (pt) REVERT: G 445 LYS cc_start: 0.7965 (tptt) cc_final: 0.7447 (pttt) REVERT: H 380 ILE cc_start: 0.1260 (mm) cc_final: 0.0714 (tt) REVERT: H 453 ASP cc_start: 0.7804 (t0) cc_final: 0.7478 (t0) REVERT: K 451 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8261 (ptp90) REVERT: K 463 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7470 (tm-30) REVERT: K 514 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7173 (mmm-85) REVERT: L 450 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5868 (m90) REVERT: L 451 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7764 (ttm170) REVERT: L 514 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.4864 (ptp90) REVERT: L 561 LEU cc_start: 0.8744 (tt) cc_final: 0.8367 (pp) REVERT: L 570 ASP cc_start: 0.8324 (t0) cc_final: 0.8055 (t0) REVERT: R 90 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7511 (tm-30) REVERT: R 109 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7500 (t0) REVERT: R 112 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7329 (ptm160) outliers start: 83 outliers final: 63 residues processed: 313 average time/residue: 0.1720 time to fit residues: 78.6624 Evaluate side-chains 316 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 243 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 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 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 447 VAL 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 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 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 489 MET 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 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 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 514 ARG Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 191 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 92 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 192 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 = 0.4513 r_free = 0.4513 target = 0.201770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121013 restraints weight = 27106.514| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.81 r_work: 0.3354 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19841 Z= 0.179 Angle : 0.662 12.584 27182 Z= 0.328 Chirality : 0.048 0.366 3221 Planarity : 0.005 0.060 3456 Dihedral : 5.837 57.125 2685 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.72 % Allowed : 20.16 % Favored : 76.11 % 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 are not related in a simple way. whole: -1.57 (0.17), residues: 2438 helix: -1.50 (0.38), residues: 158 sheet: -0.18 (0.17), residues: 894 loop : -1.60 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 443 TYR 0.013 0.001 TYR L 534 PHE 0.020 0.002 PHE E 424 TRP 0.035 0.001 TRP B 382 HIS 0.006 0.001 HIS K 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (19802) covalent geometry : angle 0.63855 / 0.32 (27093) SS BOND : bond 0.00410 / 0.26 ( 28) SS BOND : angle 1.76100 / 1.17 ( 56) hydrogen bonds : bond 0.03134 / 2.11 ( 532) hydrogen bonds : angle 5.21025 / 3.62 ( 1494) link_NAG-ASN : bond 0.00765 / 0.52 ( 11) link_NAG-ASN : angle 4.51896 / 3.14 ( 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 319 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 0.795 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 529 ASN cc_start: 0.8634 (m-40) cc_final: 0.8374 (p0) REVERT: A 537 VAL cc_start: 0.9138 (OUTLIER) cc_final: 0.8829 (m) REVERT: B 461 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7303 (tpp-160) REVERT: B 490 GLN cc_start: 0.8084 (tt0) cc_final: 0.7810 (tt0) REVERT: B 510 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7971 (pp30) REVERT: C 391 LYS cc_start: 0.7388 (tmtt) cc_final: 0.6539 (ttmm) REVERT: D 439 GLN cc_start: 0.5452 (tp40) cc_final: 0.4955 (tm-30) REVERT: D 443 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.7012 (ttp-110) REVERT: D 453 ASP cc_start: 0.8492 (m-30) cc_final: 0.8127 (m-30) REVERT: D 489 MET cc_start: 0.8626 (mtm) cc_final: 0.8049 (mtt) REVERT: D 498 GLU cc_start: 0.8821 (pt0) cc_final: 0.8337 (pm20) REVERT: D 534 TYR cc_start: 0.8087 (m-10) cc_final: 0.7850 (m-80) REVERT: E 391 LYS cc_start: 0.7659 (tptp) cc_final: 0.7381 (pttt) REVERT: E 554 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7438 (tptp) REVERT: F 449 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7975 (pp) REVERT: F 453 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7523 (p0) REVERT: F 461 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7517 (mtt180) REVERT: F 527 GLU cc_start: 0.8292 (mp0) cc_final: 0.8070 (mp0) REVERT: F 561 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7545 (tt) REVERT: G 364 LYS cc_start: 0.7703 (tptt) cc_final: 0.7397 (tppt) REVERT: G 441 ILE cc_start: 0.4535 (OUTLIER) cc_final: 0.4233 (pt) REVERT: G 445 LYS cc_start: 0.7986 (tptt) cc_final: 0.7519 (pttt) REVERT: H 380 ILE cc_start: 0.1261 (mm) cc_final: 0.0711 (tt) REVERT: K 451 ARG cc_start: 0.8531 (ptm-80) cc_final: 0.8163 (ptp-170) REVERT: K 463 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7471 (tm-30) REVERT: K 514 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7209 (mmm-85) REVERT: L 450 HIS cc_start: 0.6067 (OUTLIER) cc_final: 0.5779 (m90) REVERT: L 451 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7778 (ttm170) REVERT: L 561 LEU cc_start: 0.8764 (tt) cc_final: 0.8294 (pp) REVERT: L 570 ASP cc_start: 0.8326 (t0) cc_final: 0.8074 (t0) REVERT: R 90 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7502 (tm-30) REVERT: R 109 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7496 (t0) REVERT: R 112 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7199 (ptm160) outliers start: 82 outliers final: 66 residues processed: 297 average time/residue: 0.1723 time to fit residues: 74.4504 Evaluate side-chains 309 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 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 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 E residue 453 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 VAL 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 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 456 LEU 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 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 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 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 108 MET 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 74 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.203973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.123972 restraints weight = 27342.680| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.79 r_work: 0.3395 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19841 Z= 0.117 Angle : 0.636 11.794 27182 Z= 0.314 Chirality : 0.046 0.342 3221 Planarity : 0.005 0.059 3456 Dihedral : 5.709 56.055 2685 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.41 % Allowed : 20.39 % Favored : 76.20 % 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 are not related in a simple way. whole: -1.48 (0.17), residues: 2438 helix: -1.54 (0.38), residues: 163 sheet: -0.15 (0.17), residues: 909 loop : -1.52 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 514 TYR 0.013 0.001 TYR K 534 PHE 0.021 0.001 PHE E 424 TRP 0.038 0.001 TRP B 382 HIS 0.004 0.001 HIS G 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19802) covalent geometry : angle 0.61497 / 0.31 (27093) SS BOND : bond 0.00379 / 0.25 ( 28) SS BOND : angle 1.51135 / 1.01 ( 56) hydrogen bonds : bond 0.02950 / 2.00 ( 532) hydrogen bonds : angle 5.09058 / 3.53 ( 1494) link_NAG-ASN : bond 0.00785 / 0.54 ( 11) link_NAG-ASN : angle 4.35664 / 3.11 ( 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 319 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 0.816 Fit side-chains 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 529 ASN cc_start: 0.8639 (m-40) cc_final: 0.8398 (p0) REVERT: A 537 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8786 (m) REVERT: B 461 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7207 (tpp-160) REVERT: B 490 GLN cc_start: 0.7986 (tt0) cc_final: 0.7748 (tt0) REVERT: C 391 LYS cc_start: 0.7358 (tmtt) cc_final: 0.6488 (ttmm) REVERT: C 489 MET cc_start: 0.8565 (mtt) cc_final: 0.8342 (mtt) REVERT: D 439 GLN cc_start: 0.5503 (tp40) cc_final: 0.5259 (tm-30) REVERT: D 489 MET cc_start: 0.8579 (mtm) cc_final: 0.8027 (mtt) REVERT: D 498 GLU cc_start: 0.8846 (pt0) cc_final: 0.8352 (pm20) REVERT: E 391 LYS cc_start: 0.7606 (tptp) cc_final: 0.7320 (pttt) REVERT: E 554 LYS cc_start: 0.8262 (tmtt) cc_final: 0.7307 (tptp) REVERT: F 449 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7925 (pp) REVERT: F 453 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7499 (p0) REVERT: F 462 GLU cc_start: 0.8470 (mp0) cc_final: 0.8172 (mt-10) REVERT: F 527 GLU cc_start: 0.8282 (mp0) cc_final: 0.8067 (mp0) REVERT: F 561 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7481 (tt) REVERT: G 364 LYS cc_start: 0.7716 (tptt) cc_final: 0.7423 (tppt) REVERT: G 441 ILE cc_start: 0.4443 (OUTLIER) cc_final: 0.4196 (pt) REVERT: G 445 LYS cc_start: 0.8005 (tptt) cc_final: 0.7492 (pttt) REVERT: H 380 ILE cc_start: 0.1423 (mm) cc_final: 0.0857 (tt) REVERT: K 451 ARG cc_start: 0.8508 (ptm-80) cc_final: 0.8203 (ptp90) REVERT: K 463 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7404 (tm-30) REVERT: K 514 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7123 (mmm-85) REVERT: L 514 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4909 (ptp90) REVERT: L 561 LEU cc_start: 0.8727 (tt) cc_final: 0.8359 (pp) REVERT: L 567 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7484 (p) REVERT: L 570 ASP cc_start: 0.8292 (t0) cc_final: 0.8049 (t0) REVERT: R 73 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8057 (mmmt) REVERT: R 90 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7483 (tm-30) REVERT: R 109 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7784 (t0) REVERT: R 112 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7274 (ptm160) outliers start: 75 outliers final: 61 residues processed: 297 average time/residue: 0.1720 time to fit residues: 74.6700 Evaluate side-chains 309 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 422 GLU Chi-restraints excluded: chain C residue 425 THR 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 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 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 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 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 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 537 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 108 MET 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: 9.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 1 optimal weight: 0.0060 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** C 430 HIS ** 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** ** 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 = 0.4504 r_free = 0.4504 target = 0.200612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119742 restraints weight = 27352.424| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.81 r_work: 0.3334 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19841 Z= 0.205 Angle : 0.689 12.829 27182 Z= 0.342 Chirality : 0.049 0.373 3221 Planarity : 0.005 0.059 3456 Dihedral : 5.665 57.109 2677 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.41 % Allowed : 20.66 % 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 are not related in a simple way. whole: -1.55 (0.17), residues: 2438 helix: -1.45 (0.39), residues: 157 sheet: -0.18 (0.17), residues: 896 loop : -1.60 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 514 TYR 0.023 0.002 TYR H 455 PHE 0.020 0.002 PHE E 424 TRP 0.036 0.001 TRP B 382 HIS 0.006 0.001 HIS L 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (19802) covalent geometry : angle 0.66753 / 0.34 (27093) SS BOND : bond 0.00451 / 0.27 ( 28) SS BOND : angle 1.75323 / 1.16 ( 56) hydrogen bonds : bond 0.03252 / 2.20 ( 532) hydrogen bonds : angle 5.26184 / 3.64 ( 1494) link_NAG-ASN : bond 0.00744 / 0.50 ( 11) link_NAG-ASN : angle 4.52913 / 3.10 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6517.41 seconds wall clock time: 112 minutes 7.01 seconds (6727.01 seconds total)