Starting phenix.real_space_refine on Tue Jun 17 01:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.map" model { file = "/net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ytc_34085/06_2025/7ytc_34085.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19328 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 825 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.28, per 1000 atoms: 0.69 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: 4.85 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.80 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: 6.26 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3154 1.25 - 1.40: 4597 1.40 - 1.54: 11748 1.54 - 1.68: 174 1.68 - 1.83: 129 Bond restraints: 19802 Sorted by residual: bond pdb=" CA ASN H 563 " pdb=" C ASN H 563 " ideal model delta sigma weight residual 1.524 1.389 0.134 1.30e-02 5.92e+03 1.07e+02 bond pdb=" C ASN H 563 " pdb=" O ASN H 563 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.22e-02 6.72e+03 1.02e+02 bond pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 1.520 1.406 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C ILE J 39 " pdb=" O ILE J 39 " ideal model delta sigma weight residual 1.238 1.137 0.100 1.06e-02 8.90e+03 8.98e+01 bond pdb=" C VAL C 564 " pdb=" O VAL C 564 " ideal model delta sigma weight residual 1.237 1.146 0.091 9.80e-03 1.04e+04 8.59e+01 ... (remaining 19797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 26622 4.39 - 8.79: 395 8.79 - 13.18: 53 13.18 - 17.57: 20 17.57 - 21.97: 3 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N THR B 533 " pdb=" CA THR B 533 " pdb=" C THR B 533 " ideal model delta sigma weight residual 111.28 133.25 -21.97 1.09e+00 8.42e-01 4.06e+02 angle pdb=" N THR K 533 " pdb=" CA THR K 533 " pdb=" C THR K 533 " ideal model delta sigma weight residual 111.28 127.21 -15.93 1.09e+00 8.42e-01 2.14e+02 angle pdb=" C SER L 496 " pdb=" N PRO L 497 " pdb=" CA PRO L 497 " ideal model delta sigma weight residual 119.87 134.35 -14.48 1.04e+00 9.25e-01 1.94e+02 angle pdb=" C LYS F 558 " pdb=" N PRO F 559 " pdb=" CA PRO F 559 " ideal model delta sigma weight residual 119.05 134.25 -15.20 1.11e+00 8.12e-01 1.88e+02 angle pdb=" N PRO B 452 " pdb=" CA PRO B 452 " pdb=" C PRO B 452 " ideal model delta sigma weight residual 113.84 130.83 -16.99 1.30e+00 5.92e-01 1.71e+02 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 11027 21.57 - 43.15: 902 43.15 - 64.72: 217 64.72 - 86.29: 40 86.29 - 107.87: 10 Dihedral angle restraints: 12196 sinusoidal: 4949 harmonic: 7247 Sorted by residual: dihedral pdb=" C THR F 560 " pdb=" N THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual -122.00 -151.55 29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual 123.40 151.69 -28.29 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C ASN R 85 " pdb=" N ASN R 85 " pdb=" CA ASN R 85 " pdb=" CB ASN R 85 " ideal model delta harmonic sigma weight residual -122.60 -146.78 24.18 0 2.50e+00 1.60e-01 9.36e+01 ... (remaining 12193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3161 0.270 - 0.540: 51 0.540 - 0.809: 7 0.809 - 1.079: 1 1.079 - 1.349: 1 Chirality restraints: 3221 Sorted by residual: chirality pdb=" CA THR F 560 " pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CB THR F 560 " both_signs ideal model delta sigma weight residual False 2.53 1.18 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA ASN R 85 " pdb=" N ASN R 85 " pdb=" C ASN R 85 " pdb=" CB ASN R 85 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA THR B 533 " pdb=" N THR B 533 " pdb=" C THR B 533 " pdb=" CB THR B 533 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3218 not shown) Planarity restraints: 3467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 558 " -0.101 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO K 559 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO K 559 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO K 559 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 562 " 0.030 2.00e-02 2.50e+03 5.98e-02 3.57e+01 pdb=" C TYR C 562 " -0.103 2.00e-02 2.50e+03 pdb=" O TYR C 562 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN C 563 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 488 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C TRP B 488 " -0.095 2.00e-02 2.50e+03 pdb=" O TRP B 488 " 0.036 2.00e-02 2.50e+03 pdb=" N MET B 489 " 0.033 2.00e-02 2.50e+03 ... (remaining 3464 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 28 1.95 - 2.68: 1065 2.68 - 3.42: 25865 3.42 - 4.16: 44293 4.16 - 4.90: 76988 Nonbonded interactions: 148239 Sorted by model distance: nonbonded pdb=" NH1 ARG C 384 " pdb=" O ALA C 389 " model vdw 1.208 3.120 nonbonded pdb=" O ARG L 491 " pdb=" NE2 GLN L 493 " model vdw 1.411 3.120 nonbonded pdb=" OD2 ASP E 453 " pdb=" CE2 TYR E 455 " model vdw 1.433 3.340 nonbonded pdb=" OD2 ASP E 453 " pdb=" CZ TYR E 455 " model vdw 1.501 3.260 nonbonded pdb=" OD1 ASN C 386 " pdb=" CG GLU C 388 " model vdw 1.537 3.440 ... (remaining 148234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 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 568 or res \ id 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 568 or res \ id 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 568 or resid 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 568 or res \ id 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: 2.480 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.390 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 19841 Z= 0.733 Angle : 1.397 37.574 27182 Z= 0.841 Chirality : 0.087 1.349 3221 Planarity : 0.008 0.151 3456 Dihedral : 16.748 107.868 7388 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer: Outliers : 8.45 % Allowed : 3.41 % Favored : 88.15 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (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 TRP 0.022 0.002 TRP G 528 HIS 0.016 0.001 HIS D 450 PHE 0.079 0.002 PHE G 479 TYR 0.047 0.003 TYR J 101 ARG 0.015 0.001 ARG F 451 Details of bonding type rmsd link_NAG-ASN : bond 0.08924 ( 11) link_NAG-ASN : angle 12.82384 ( 33) hydrogen bonds : bond 0.19892 ( 532) hydrogen bonds : angle 8.25738 ( 1494) SS BOND : bond 0.00836 ( 28) SS BOND : angle 2.24040 ( 56) covalent geometry : bond 0.01066 (19802) covalent geometry : angle 1.32177 (27093) *********************** 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 : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 364 LYS cc_start: 0.6689 (pttt) cc_final: 0.6292 (ptpt) REVERT: B 415 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: C 416 ASP cc_start: 0.9239 (m-30) cc_final: 0.9034 (p0) REVERT: C 566 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8665 (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: 97 residues processed: 464 average time/residue: 0.3781 time to fit residues: 250.2721 Evaluate side-chains 360 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 250 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 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 203 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 188 optimal weight: 0.6980 chunk 73 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 439 GLN C 450 HIS F 450 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN H 430 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.203289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123772 restraints weight = 27211.133| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.16 r_work: 0.3359 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19841 Z= 0.175 Angle : 0.734 12.842 27182 Z= 0.368 Chirality : 0.050 0.410 3221 Planarity : 0.006 0.085 3456 Dihedral : 11.084 88.611 3106 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.57 % Favored : 91.39 % Rotamer: Outliers : 4.59 % Allowed : 11.31 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2438 helix: -2.47 (0.31), residues: 167 sheet: -0.79 (0.17), residues: 893 loop : -2.04 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 382 HIS 0.008 0.001 HIS L 518 PHE 0.025 0.002 PHE B 348 TYR 0.029 0.002 TYR C 534 ARG 0.006 0.001 ARG R 45 Details of bonding type rmsd link_NAG-ASN : bond 0.01036 ( 11) link_NAG-ASN : angle 5.21843 ( 33) hydrogen bonds : bond 0.04096 ( 532) hydrogen bonds : angle 6.39999 ( 1494) SS BOND : bond 0.00459 ( 28) SS BOND : angle 1.22452 ( 56) covalent geometry : bond 0.00404 (19802) covalent geometry : angle 0.71015 (27093) *********************** 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 383 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 282 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7605 (pptt) REVERT: B 461 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7284 (tpp-160) REVERT: B 489 MET cc_start: 0.8239 (mtt) cc_final: 0.7876 (mtt) REVERT: B 490 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: B 499 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8197 (mttt) REVERT: B 510 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7983 (pp30) REVERT: B 546 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7758 (ttm170) REVERT: D 424 PHE cc_start: 0.8453 (m-80) cc_final: 0.8198 (m-80) REVERT: D 489 MET cc_start: 0.8277 (mtm) cc_final: 0.7802 (mtt) REVERT: D 534 TYR cc_start: 0.8066 (m-80) cc_final: 0.7818 (m-80) REVERT: E 453 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6897 (p0) REVERT: E 500 TYR cc_start: 0.9065 (p90) cc_final: 0.8784 (p90) REVERT: E 514 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8140 (mpp80) REVERT: E 554 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7450 (tmtt) REVERT: F 449 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7821 (pp) REVERT: F 453 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7291 (p0) REVERT: F 461 ARG cc_start: 0.7836 (mpp80) cc_final: 0.7367 (mtt180) REVERT: G 443 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7717 (ptm-80) REVERT: H 562 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7170 (p90) REVERT: J 106 ASN cc_start: 0.7754 (p0) cc_final: 0.7444 (m-40) REVERT: K 530 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6468 (t) REVERT: K 554 LYS cc_start: 0.8359 (tttt) cc_final: 0.7967 (tttm) REVERT: L 450 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.5666 (m90) REVERT: L 451 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: L 518 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6674 (t-170) REVERT: R 109 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7376 (t0) REVERT: R 121 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6884 (t0) outliers start: 101 outliers final: 53 residues processed: 352 average time/residue: 0.3767 time to fit residues: 190.0210 Evaluate side-chains 312 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU 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 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 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 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 92 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 214 optimal weight: 50.0000 chunk 233 optimal weight: 0.6980 chunk 111 optimal weight: 30.0000 chunk 173 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 113 optimal weight: 40.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN B 419 ASN B 439 GLN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS G 450 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 465 ASN L 493 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.198559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117233 restraints weight = 27178.474| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.74 r_work: 0.3291 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 19841 Z= 0.278 Angle : 0.778 14.906 27182 Z= 0.388 Chirality : 0.052 0.408 3221 Planarity : 0.006 0.074 3456 Dihedral : 8.996 84.194 2973 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.42 % Favored : 89.54 % Rotamer: Outliers : 4.68 % Allowed : 14.99 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2438 helix: -2.31 (0.33), residues: 158 sheet: -0.80 (0.17), residues: 874 loop : -2.14 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 418 HIS 0.006 0.001 HIS H 518 PHE 0.023 0.002 PHE G 479 TYR 0.019 0.002 TYR K 534 ARG 0.009 0.001 ARG A 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00910 ( 11) link_NAG-ASN : angle 5.59726 ( 33) hydrogen bonds : bond 0.04094 ( 532) hydrogen bonds : angle 6.20842 ( 1494) SS BOND : bond 0.00503 ( 28) SS BOND : angle 1.51313 ( 56) covalent geometry : bond 0.00668 (19802) covalent geometry : angle 0.75137 (27093) *********************** 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 363 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 260 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7906 (pptt) REVERT: B 461 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7477 (tpp-160) REVERT: B 489 MET cc_start: 0.8554 (mtt) cc_final: 0.8212 (mtp) REVERT: B 490 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: B 491 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6200 (mpt-90) REVERT: D 424 PHE cc_start: 0.8470 (m-80) cc_final: 0.7937 (m-80) REVERT: D 453 ASP cc_start: 0.8555 (m-30) cc_final: 0.8238 (m-30) REVERT: D 489 MET cc_start: 0.8528 (mtm) cc_final: 0.7951 (mtt) REVERT: E 391 LYS cc_start: 0.7753 (tptp) cc_final: 0.7175 (ttpt) REVERT: E 440 THR cc_start: 0.5844 (OUTLIER) cc_final: 0.5624 (m) REVERT: E 449 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8486 (mm) REVERT: E 451 ARG cc_start: 0.8780 (ptm-80) cc_final: 0.8568 (ptm-80) REVERT: E 453 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7212 (p0) REVERT: E 514 ARG cc_start: 0.8513 (mtt90) cc_final: 0.8167 (mpp80) REVERT: E 554 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7416 (tmtt) REVERT: F 391 LYS cc_start: 0.6138 (tptt) cc_final: 0.5885 (mmtt) REVERT: F 449 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7866 (pp) REVERT: F 453 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7749 (p0) REVERT: F 461 ARG cc_start: 0.8014 (mpp80) cc_final: 0.7513 (mtt180) REVERT: G 364 LYS cc_start: 0.7871 (tptt) cc_final: 0.7476 (tppt) REVERT: J 9 ASP cc_start: 0.8512 (t0) cc_final: 0.8125 (t0) REVERT: K 418 TRP cc_start: 0.6605 (OUTLIER) cc_final: 0.5555 (m-90) REVERT: K 514 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: K 554 LYS cc_start: 0.8484 (tttt) cc_final: 0.8116 (tttm) REVERT: L 450 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5793 (m90) REVERT: L 451 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7684 (ttm170) REVERT: L 452 PRO cc_start: 0.7047 (Cg_endo) cc_final: 0.6837 (Cg_exo) REVERT: L 518 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6696 (t-170) REVERT: R 75 ARG cc_start: 0.6298 (ptp90) cc_final: 0.5986 (ptt180) REVERT: R 90 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7439 (tm-30) REVERT: R 109 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7577 (t0) outliers start: 103 outliers final: 65 residues processed: 332 average time/residue: 0.3756 time to fit residues: 177.8756 Evaluate side-chains 315 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 236 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 414 CYS Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 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 353 SER Chi-restraints excluded: chain D residue 413 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 D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 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 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 518 HIS Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 111 optimal weight: 30.0000 chunk 13 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 193 optimal weight: 40.0000 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 463 GLN C 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.202937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122316 restraints weight = 27202.338| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.85 r_work: 0.3372 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19841 Z= 0.118 Angle : 0.652 12.515 27182 Z= 0.319 Chirality : 0.047 0.357 3221 Planarity : 0.005 0.063 3456 Dihedral : 7.859 67.517 2945 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 4.31 % Allowed : 17.08 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2438 helix: -2.12 (0.35), residues: 164 sheet: -0.54 (0.17), residues: 874 loop : -1.93 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 382 HIS 0.004 0.001 HIS L 518 PHE 0.018 0.001 PHE E 424 TYR 0.019 0.001 TYR K 534 ARG 0.008 0.000 ARG K 461 Details of bonding type rmsd link_NAG-ASN : bond 0.00893 ( 11) link_NAG-ASN : angle 5.23120 ( 33) hydrogen bonds : bond 0.03295 ( 532) hydrogen bonds : angle 5.67325 ( 1494) SS BOND : bond 0.00431 ( 28) SS BOND : angle 1.04644 ( 56) covalent geometry : bond 0.00269 (19802) covalent geometry : angle 0.62565 (27093) *********************** 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 358 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 263 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8426 (m-80) cc_final: 0.8159 (m-80) REVERT: B 445 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7966 (pptt) REVERT: B 461 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7286 (tpp-160) REVERT: B 489 MET cc_start: 0.8350 (mtt) cc_final: 0.7846 (mtt) REVERT: B 490 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 533 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7493 (t) REVERT: B 534 TYR cc_start: 0.8424 (m-80) cc_final: 0.8205 (m-80) REVERT: C 391 LYS cc_start: 0.7329 (tmtt) cc_final: 0.6513 (ttmm) REVERT: D 489 MET cc_start: 0.8545 (mtm) cc_final: 0.7980 (mtt) REVERT: D 498 GLU cc_start: 0.8813 (pt0) cc_final: 0.8316 (pm20) REVERT: E 391 LYS cc_start: 0.7640 (tptp) cc_final: 0.7115 (ttpt) REVERT: E 440 THR cc_start: 0.5921 (OUTLIER) cc_final: 0.4860 (m) REVERT: E 451 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8543 (ptm-80) REVERT: E 500 TYR cc_start: 0.9018 (p90) cc_final: 0.8742 (p90) REVERT: E 514 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8057 (mtp85) REVERT: F 449 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7870 (pp) REVERT: F 453 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7501 (p0) REVERT: F 461 ARG cc_start: 0.7962 (mpp80) cc_final: 0.7526 (mtt180) REVERT: G 364 LYS cc_start: 0.7876 (tptt) cc_final: 0.7640 (tptt) REVERT: G 443 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7349 (ptm-80) REVERT: G 445 LYS cc_start: 0.7959 (tptt) cc_final: 0.7529 (pttt) REVERT: H 380 ILE cc_start: 0.1267 (mm) cc_final: 0.0923 (tt) REVERT: J 9 ASP cc_start: 0.8438 (t0) cc_final: 0.8160 (t0) REVERT: K 418 TRP cc_start: 0.6622 (OUTLIER) cc_final: 0.4197 (t-100) REVERT: K 514 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7198 (mmm-85) REVERT: L 450 HIS cc_start: 0.6122 (OUTLIER) cc_final: 0.5746 (m90) REVERT: L 451 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7594 (ttm170) REVERT: L 561 LEU cc_start: 0.8753 (tt) cc_final: 0.8298 (pp) REVERT: L 570 ASP cc_start: 0.8416 (t0) cc_final: 0.8181 (t0) REVERT: R 90 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7434 (tm-30) REVERT: R 109 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7437 (t0) REVERT: R 112 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7229 (ptm160) outliers start: 95 outliers final: 58 residues processed: 330 average time/residue: 0.4847 time to fit residues: 233.3701 Evaluate side-chains 306 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 237 time to evaluate : 4.262 ------------------------------------------------------------------------------- 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 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 564 VAL 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 427 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 453 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 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 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 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 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 L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 197 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 220 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 0.0870 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.198542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117094 restraints weight = 27550.642| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.81 r_work: 0.3291 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 19841 Z= 0.249 Angle : 0.729 13.860 27182 Z= 0.362 Chirality : 0.051 0.416 3221 Planarity : 0.005 0.065 3456 Dihedral : 7.634 59.157 2936 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.01 % Favored : 89.95 % Rotamer: Outliers : 4.81 % Allowed : 18.03 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2438 helix: -2.04 (0.35), residues: 158 sheet: -0.65 (0.17), residues: 899 loop : -2.00 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 382 HIS 0.006 0.001 HIS K 518 PHE 0.023 0.002 PHE G 479 TYR 0.015 0.002 TYR K 534 ARG 0.006 0.001 ARG F 451 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 11) link_NAG-ASN : angle 5.60292 ( 33) hydrogen bonds : bond 0.03670 ( 532) hydrogen bonds : angle 5.79127 ( 1494) SS BOND : bond 0.00524 ( 28) SS BOND : angle 1.39645 ( 56) covalent geometry : bond 0.00598 (19802) covalent geometry : angle 0.70104 (27093) *********************** 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 355 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 249 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8544 (tptm) REVERT: B 445 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7979 (pptt) REVERT: B 461 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7464 (tpp-160) REVERT: B 489 MET cc_start: 0.8541 (mtt) cc_final: 0.8073 (mtt) REVERT: B 490 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 533 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7412 (t) REVERT: D 453 ASP cc_start: 0.8507 (m-30) cc_final: 0.8198 (m-30) REVERT: D 489 MET cc_start: 0.8637 (mtm) cc_final: 0.8043 (mtt) REVERT: E 391 LYS cc_start: 0.7668 (tptp) cc_final: 0.7166 (ttpt) REVERT: E 440 THR cc_start: 0.5454 (OUTLIER) cc_final: 0.5240 (m) REVERT: E 514 ARG cc_start: 0.8498 (mtt90) cc_final: 0.8124 (mtp85) REVERT: F 449 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7939 (pp) REVERT: F 453 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7619 (p0) REVERT: G 364 LYS cc_start: 0.7865 (tptt) cc_final: 0.7240 (tppt) REVERT: G 443 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7253 (ptm-80) REVERT: G 445 LYS cc_start: 0.7967 (tptt) cc_final: 0.7555 (pttt) REVERT: H 380 ILE cc_start: 0.1270 (mm) cc_final: 0.0939 (tt) REVERT: H 453 ASP cc_start: 0.8016 (t0) cc_final: 0.7686 (t0) REVERT: J 9 ASP cc_start: 0.8535 (t0) cc_final: 0.8184 (t0) REVERT: K 418 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.3994 (t-100) REVERT: K 451 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8148 (ptp-170) REVERT: K 463 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7425 (tm-30) REVERT: K 514 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7215 (mmm-85) REVERT: L 450 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5631 (m90) REVERT: L 451 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7726 (ttm170) REVERT: L 561 LEU cc_start: 0.8722 (tt) cc_final: 0.8139 (pp) REVERT: L 570 ASP cc_start: 0.8361 (t0) cc_final: 0.8089 (t0) REVERT: R 90 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7385 (tm-30) REVERT: R 109 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7688 (t0) REVERT: R 112 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7250 (ptm160) outliers start: 106 outliers final: 78 residues processed: 325 average time/residue: 0.5162 time to fit residues: 244.4580 Evaluate side-chains 325 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 236 time to evaluate : 2.890 ------------------------------------------------------------------------------- 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 480 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS 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 518 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 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 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 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 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 1 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 203 optimal weight: 0.0170 chunk 234 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 187 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 545 ASN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 493 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.199004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117532 restraints weight = 27401.111| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.80 r_work: 0.3302 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19841 Z= 0.214 Angle : 0.704 14.030 27182 Z= 0.347 Chirality : 0.050 0.397 3221 Planarity : 0.005 0.063 3456 Dihedral : 7.492 59.684 2935 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.95 % Allowed : 18.98 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2438 helix: -1.77 (0.37), residues: 158 sheet: -0.63 (0.17), residues: 896 loop : -1.93 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 382 HIS 0.006 0.001 HIS H 518 PHE 0.021 0.002 PHE E 424 TYR 0.015 0.002 TYR K 534 ARG 0.006 0.001 ARG K 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 11) link_NAG-ASN : angle 5.55107 ( 33) hydrogen bonds : bond 0.03455 ( 532) hydrogen bonds : angle 5.68555 ( 1494) SS BOND : bond 0.00385 ( 28) SS BOND : angle 1.45009 ( 56) covalent geometry : bond 0.00515 (19802) covalent geometry : angle 0.67474 (27093) *********************** 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 364 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 255 time to evaluate : 2.274 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: A 554 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8532 (tptm) REVERT: B 445 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: B 461 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7389 (tpp-160) REVERT: B 489 MET cc_start: 0.8523 (mtt) cc_final: 0.7994 (mtt) REVERT: B 490 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: B 533 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7411 (t) REVERT: C 371 ASP cc_start: 0.6474 (t70) cc_final: 0.6146 (m-30) REVERT: C 391 LYS cc_start: 0.7376 (tmtt) cc_final: 0.6566 (ttmm) REVERT: D 453 ASP cc_start: 0.8498 (m-30) cc_final: 0.8191 (m-30) REVERT: D 489 MET cc_start: 0.8663 (mtm) cc_final: 0.8060 (mtt) REVERT: E 391 LYS cc_start: 0.7723 (tptp) cc_final: 0.7249 (ttpt) REVERT: F 449 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7988 (pp) REVERT: F 453 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7545 (p0) REVERT: F 461 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7867 (mtt180) REVERT: G 364 LYS cc_start: 0.7865 (tptt) cc_final: 0.7190 (tppt) REVERT: G 443 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7545 (ptm-80) REVERT: G 445 LYS cc_start: 0.7955 (tptt) cc_final: 0.7571 (pttt) REVERT: H 380 ILE cc_start: 0.1347 (mm) cc_final: 0.1021 (tt) REVERT: H 453 ASP cc_start: 0.7993 (t0) cc_final: 0.7708 (t0) REVERT: J 9 ASP cc_start: 0.8575 (t0) cc_final: 0.8255 (t0) REVERT: K 418 TRP cc_start: 0.6627 (OUTLIER) cc_final: 0.3821 (t-100) REVERT: K 451 ARG cc_start: 0.8502 (ptm-80) cc_final: 0.8156 (ptp-170) REVERT: K 463 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7370 (tm-30) REVERT: K 514 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.6886 (mtp85) REVERT: L 450 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5622 (m90) REVERT: L 451 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: L 490 GLN cc_start: 0.5317 (tt0) cc_final: 0.4712 (tt0) REVERT: L 493 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: L 561 LEU cc_start: 0.8745 (tt) cc_final: 0.8297 (pp) REVERT: L 570 ASP cc_start: 0.8310 (t0) cc_final: 0.8054 (t0) REVERT: R 90 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7431 (tm-30) REVERT: R 109 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7694 (t0) REVERT: R 112 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7374 (ptm160) outliers start: 109 outliers final: 75 residues processed: 333 average time/residue: 0.3936 time to fit residues: 189.4706 Evaluate side-chains 323 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 GLN Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 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 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 453 ASP 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 G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain 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 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 15 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 147 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.200344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119352 restraints weight = 27238.340| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.79 r_work: 0.3333 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19841 Z= 0.151 Angle : 0.676 13.477 27182 Z= 0.331 Chirality : 0.048 0.380 3221 Planarity : 0.005 0.062 3456 Dihedral : 7.198 59.347 2932 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.68 % Allowed : 19.98 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2438 helix: -1.84 (0.36), residues: 157 sheet: -0.53 (0.17), residues: 895 loop : -1.78 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 382 HIS 0.006 0.001 HIS G 430 PHE 0.025 0.002 PHE L 516 TYR 0.014 0.001 TYR K 534 ARG 0.009 0.001 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 11) link_NAG-ASN : angle 5.37468 ( 33) hydrogen bonds : bond 0.03245 ( 532) hydrogen bonds : angle 5.54285 ( 1494) SS BOND : bond 0.00405 ( 28) SS BOND : angle 1.88410 ( 56) covalent geometry : bond 0.00355 (19802) covalent geometry : angle 0.64486 (27093) *********************** 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 357 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 254 time to evaluate : 2.070 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: A 525 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 529 ASN cc_start: 0.8621 (m-40) cc_final: 0.8395 (p0) REVERT: B 445 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8020 (pptt) REVERT: B 461 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7339 (tpp-160) REVERT: B 489 MET cc_start: 0.8447 (mtt) cc_final: 0.8040 (mtp) REVERT: B 490 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: B 510 GLN cc_start: 0.8422 (pp30) cc_final: 0.8004 (pp30) REVERT: B 533 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7383 (t) REVERT: C 371 ASP cc_start: 0.6520 (t70) cc_final: 0.6200 (m-30) REVERT: C 391 LYS cc_start: 0.7379 (tmtt) cc_final: 0.6540 (ttmm) REVERT: D 489 MET cc_start: 0.8654 (mtm) cc_final: 0.8071 (mtt) REVERT: E 391 LYS cc_start: 0.7687 (tptp) cc_final: 0.7234 (ttpt) REVERT: F 449 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8022 (pp) REVERT: F 453 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7524 (p0) REVERT: F 461 ARG cc_start: 0.8062 (mpp80) cc_final: 0.7707 (mtt180) REVERT: G 364 LYS cc_start: 0.7738 (tptt) cc_final: 0.7350 (tppt) REVERT: G 443 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7438 (ptm-80) REVERT: G 445 LYS cc_start: 0.7990 (tptt) cc_final: 0.7574 (pttt) REVERT: H 380 ILE cc_start: 0.1336 (mm) cc_final: 0.0987 (tt) REVERT: H 453 ASP cc_start: 0.7946 (t0) cc_final: 0.7637 (t0) REVERT: H 534 TYR cc_start: 0.8928 (m-80) cc_final: 0.8421 (m-80) REVERT: J 9 ASP cc_start: 0.8565 (t0) cc_final: 0.8228 (t0) REVERT: K 391 LYS cc_start: 0.5174 (tptt) cc_final: 0.4825 (tppt) REVERT: K 418 TRP cc_start: 0.6563 (OUTLIER) cc_final: 0.3678 (t-100) REVERT: K 451 ARG cc_start: 0.8496 (ptm-80) cc_final: 0.8155 (ptp-170) REVERT: K 463 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7322 (tm-30) REVERT: K 467 ARG cc_start: 0.7952 (tpp80) cc_final: 0.7687 (tpp80) REVERT: K 514 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.6877 (mtp85) REVERT: L 450 HIS cc_start: 0.6050 (OUTLIER) cc_final: 0.5598 (m90) REVERT: L 451 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: L 490 GLN cc_start: 0.5670 (tt0) cc_final: 0.5440 (tt0) REVERT: L 561 LEU cc_start: 0.8708 (tt) cc_final: 0.8335 (pp) REVERT: L 570 ASP cc_start: 0.8308 (t0) cc_final: 0.8042 (t0) REVERT: R 90 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7462 (tm-30) REVERT: R 109 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7699 (t0) REVERT: R 112 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7203 (ptm160) outliers start: 103 outliers final: 73 residues processed: 326 average time/residue: 0.3723 time to fit residues: 172.8861 Evaluate side-chains 321 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 238 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 419 ASN 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 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 393 HIS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 567 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 537 VAL Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 461 ARG Chi-restraints excluded: chain H residue 462 GLU 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 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 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 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 56 optimal weight: 0.1980 chunk 216 optimal weight: 0.9990 chunk 89 optimal weight: 30.0000 chunk 109 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 chunk 217 optimal weight: 30.0000 chunk 172 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 463 GLN D 518 HIS ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.201940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131470 restraints weight = 27269.070| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 4.62 r_work: 0.3302 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19841 Z= 0.122 Angle : 0.651 13.180 27182 Z= 0.319 Chirality : 0.047 0.375 3221 Planarity : 0.005 0.058 3456 Dihedral : 6.829 59.422 2928 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.04 % Allowed : 20.25 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2438 helix: -1.72 (0.37), residues: 157 sheet: -0.37 (0.17), residues: 891 loop : -1.70 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 382 HIS 0.018 0.001 HIS C 393 PHE 0.024 0.001 PHE L 516 TYR 0.014 0.001 TYR K 534 ARG 0.008 0.001 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 11) link_NAG-ASN : angle 5.21032 ( 33) hydrogen bonds : bond 0.03109 ( 532) hydrogen bonds : angle 5.32461 ( 1494) SS BOND : bond 0.00378 ( 28) SS BOND : angle 1.49800 ( 56) covalent geometry : bond 0.00281 (19802) covalent geometry : angle 0.62201 (27093) *********************** 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 345 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 256 time to evaluate : 1.971 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: B 445 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8071 (pptt) REVERT: B 461 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7409 (tpp-160) REVERT: B 489 MET cc_start: 0.8350 (mtt) cc_final: 0.7989 (mtp) REVERT: B 490 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 371 ASP cc_start: 0.6474 (t70) cc_final: 0.6129 (m-30) REVERT: C 489 MET cc_start: 0.8747 (mtt) cc_final: 0.8503 (mtt) REVERT: D 414 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6380 (m) REVERT: D 489 MET cc_start: 0.8677 (mtm) cc_final: 0.8133 (mtt) REVERT: D 498 GLU cc_start: 0.8870 (pt0) cc_final: 0.8392 (pm20) REVERT: E 391 LYS cc_start: 0.7682 (tptp) cc_final: 0.7384 (pttt) REVERT: E 500 TYR cc_start: 0.9055 (p90) cc_final: 0.8766 (p90) REVERT: E 554 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7521 (tmtt) REVERT: F 449 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8036 (pp) REVERT: F 451 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8243 (mtp-110) REVERT: F 453 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7626 (p0) REVERT: F 461 ARG cc_start: 0.8041 (mpp80) cc_final: 0.7719 (mtt180) REVERT: G 443 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7658 (ptm-80) REVERT: G 445 LYS cc_start: 0.8011 (tptt) cc_final: 0.7599 (pttt) REVERT: H 380 ILE cc_start: 0.1499 (mm) cc_final: 0.1010 (tt) REVERT: H 453 ASP cc_start: 0.8039 (t0) cc_final: 0.7742 (t0) REVERT: J 9 ASP cc_start: 0.8510 (t0) cc_final: 0.8208 (t0) REVERT: K 463 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7379 (tm-30) REVERT: K 467 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7655 (tpp80) REVERT: K 514 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7263 (mmm-85) REVERT: L 450 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5596 (m90) REVERT: L 451 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7753 (ttm170) REVERT: L 490 GLN cc_start: 0.5685 (tt0) cc_final: 0.5460 (tt0) REVERT: L 561 LEU cc_start: 0.8707 (tt) cc_final: 0.8436 (pp) REVERT: L 570 ASP cc_start: 0.8339 (t0) cc_final: 0.8065 (t0) REVERT: R 90 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7551 (tm-30) REVERT: R 109 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7809 (t0) REVERT: R 112 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7258 (ptm160) outliers start: 89 outliers final: 69 residues processed: 316 average time/residue: 0.3755 time to fit residues: 169.7217 Evaluate side-chains 321 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 243 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 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 D residue 567 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 537 VAL Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 461 ARG 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 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 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 130 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 0.0050 chunk 197 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 109 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 HIS C 463 GLN G 545 ASN ** K 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.202952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133675 restraints weight = 27147.400| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.55 r_work: 0.3312 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19841 Z= 0.114 Angle : 0.648 12.807 27182 Z= 0.318 Chirality : 0.046 0.372 3221 Planarity : 0.005 0.058 3456 Dihedral : 6.519 58.034 2922 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.95 % Allowed : 20.66 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2438 helix: -1.59 (0.38), residues: 157 sheet: -0.26 (0.17), residues: 898 loop : -1.61 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 382 HIS 0.005 0.001 HIS C 393 PHE 0.024 0.001 PHE L 516 TYR 0.023 0.001 TYR R 81 ARG 0.011 0.001 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 11) link_NAG-ASN : angle 5.08459 ( 33) hydrogen bonds : bond 0.03022 ( 532) hydrogen bonds : angle 5.14532 ( 1494) SS BOND : bond 0.00393 ( 28) SS BOND : angle 1.29857 ( 56) covalent geometry : bond 0.00262 (19802) covalent geometry : angle 0.62169 (27093) *********************** 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 344 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 257 time to evaluate : 2.209 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: B 461 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7407 (tpp-160) REVERT: C 371 ASP cc_start: 0.6491 (t70) cc_final: 0.6156 (m-30) REVERT: C 489 MET cc_start: 0.8780 (mtt) cc_final: 0.8489 (mtt) REVERT: D 414 CYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6362 (m) REVERT: D 489 MET cc_start: 0.8662 (mtm) cc_final: 0.8122 (mtt) REVERT: D 498 GLU cc_start: 0.8867 (pt0) cc_final: 0.8394 (pm20) REVERT: E 391 LYS cc_start: 0.7647 (tptp) cc_final: 0.7365 (pttt) REVERT: E 500 TYR cc_start: 0.9045 (p90) cc_final: 0.8742 (p90) REVERT: E 514 ARG cc_start: 0.8448 (mtt90) cc_final: 0.8040 (mtp85) REVERT: F 449 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8016 (pp) REVERT: F 453 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7621 (p0) REVERT: F 461 ARG cc_start: 0.8044 (mpp80) cc_final: 0.7720 (mtt180) REVERT: G 441 ILE cc_start: 0.4528 (OUTLIER) cc_final: 0.4176 (pt) REVERT: G 445 LYS cc_start: 0.8013 (tptt) cc_final: 0.7526 (pttt) REVERT: H 380 ILE cc_start: 0.1485 (mm) cc_final: 0.1005 (tt) REVERT: H 453 ASP cc_start: 0.8057 (t0) cc_final: 0.7658 (t0) REVERT: H 534 TYR cc_start: 0.8960 (m-80) cc_final: 0.8526 (m-80) REVERT: J 9 ASP cc_start: 0.8504 (t0) cc_final: 0.8197 (t0) REVERT: K 451 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8268 (ptp90) REVERT: K 463 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7394 (tm-30) REVERT: K 514 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7252 (mmm-85) REVERT: L 450 HIS cc_start: 0.5994 (OUTLIER) cc_final: 0.5620 (m90) REVERT: L 451 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7645 (ttm170) REVERT: L 490 GLN cc_start: 0.5684 (tt0) cc_final: 0.5466 (tt0) REVERT: L 561 LEU cc_start: 0.8693 (tt) cc_final: 0.8474 (pp) REVERT: L 570 ASP cc_start: 0.8368 (t0) cc_final: 0.8085 (t0) REVERT: R 109 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7742 (t0) REVERT: R 112 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7227 (ptm160) outliers start: 87 outliers final: 66 residues processed: 317 average time/residue: 0.3750 time to fit residues: 172.0088 Evaluate side-chains 315 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 242 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 447 VAL 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 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 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 567 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 537 VAL Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 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 461 ARG 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 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 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 240 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.201581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126970 restraints weight = 27270.965| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.50 r_work: 0.3297 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19841 Z= 0.144 Angle : 0.666 13.443 27182 Z= 0.328 Chirality : 0.047 0.385 3221 Planarity : 0.005 0.055 3456 Dihedral : 6.382 58.046 2915 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.59 % Allowed : 20.98 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2438 helix: -1.53 (0.39), residues: 157 sheet: -0.24 (0.17), residues: 905 loop : -1.57 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 382 HIS 0.004 0.001 HIS G 430 PHE 0.025 0.002 PHE E 424 TYR 0.013 0.001 TYR K 534 ARG 0.010 0.001 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 11) link_NAG-ASN : angle 5.13803 ( 33) hydrogen bonds : bond 0.03091 ( 532) hydrogen bonds : angle 5.15428 ( 1494) SS BOND : bond 0.00379 ( 28) SS BOND : angle 1.34554 ( 56) covalent geometry : bond 0.00340 (19802) covalent geometry : angle 0.63967 (27093) ********************** 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 327 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 2.075 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: A 529 ASN cc_start: 0.8689 (m-40) cc_final: 0.8363 (p0) REVERT: B 461 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7292 (tpp-160) REVERT: B 490 GLN cc_start: 0.8031 (tt0) cc_final: 0.7755 (tt0) REVERT: B 533 THR cc_start: 0.7780 (m) cc_final: 0.7540 (t) REVERT: C 371 ASP cc_start: 0.6558 (t70) cc_final: 0.6217 (m-30) REVERT: C 391 LYS cc_start: 0.7393 (tmtt) cc_final: 0.6615 (ttmm) REVERT: C 489 MET cc_start: 0.8802 (mtt) cc_final: 0.8472 (mtt) REVERT: D 414 CYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6439 (m) REVERT: D 489 MET cc_start: 0.8672 (mtm) cc_final: 0.8107 (mtt) REVERT: D 498 GLU cc_start: 0.8881 (pt0) cc_final: 0.8384 (pm20) REVERT: E 391 LYS cc_start: 0.7662 (tptp) cc_final: 0.7360 (pttt) REVERT: E 554 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7329 (tptp) REVERT: F 449 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7986 (pp) REVERT: F 453 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7577 (p0) REVERT: F 461 ARG cc_start: 0.8028 (mpp80) cc_final: 0.7807 (mtt180) REVERT: G 364 LYS cc_start: 0.7622 (tptt) cc_final: 0.7416 (tptt) REVERT: G 441 ILE cc_start: 0.4504 (OUTLIER) cc_final: 0.4146 (pt) REVERT: G 445 LYS cc_start: 0.8001 (tptt) cc_final: 0.7553 (pttt) REVERT: H 380 ILE cc_start: 0.1419 (mm) cc_final: 0.0923 (tt) REVERT: H 453 ASP cc_start: 0.8021 (t0) cc_final: 0.7707 (t70) REVERT: H 461 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8241 (ptm-80) REVERT: J 9 ASP cc_start: 0.8559 (t0) cc_final: 0.8267 (t0) REVERT: K 451 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8251 (ptp90) REVERT: K 463 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7361 (tm-30) REVERT: K 514 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7239 (mmm-85) REVERT: L 450 HIS cc_start: 0.5956 (OUTLIER) cc_final: 0.5600 (m90) REVERT: L 451 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7559 (ttm170) REVERT: L 561 LEU cc_start: 0.8697 (tt) cc_final: 0.8370 (pp) REVERT: L 567 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7574 (p) REVERT: L 570 ASP cc_start: 0.8397 (t0) cc_final: 0.8129 (t0) REVERT: R 109 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7658 (t0) REVERT: R 112 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7225 (ptm160) outliers start: 79 outliers final: 67 residues processed: 301 average time/residue: 0.3792 time to fit residues: 164.7982 Evaluate side-chains 321 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 245 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 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 376 ASP Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 567 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 537 VAL Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 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 461 ARG Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 465 ASN Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS 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 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 111 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 210 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.199867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119279 restraints weight = 27322.844| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.73 r_work: 0.3323 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19841 Z= 0.179 Angle : 0.690 13.733 27182 Z= 0.340 Chirality : 0.048 0.391 3221 Planarity : 0.005 0.057 3456 Dihedral : 6.579 57.996 2915 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.63 % Allowed : 20.89 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2438 helix: -1.60 (0.38), residues: 159 sheet: -0.27 (0.17), residues: 889 loop : -1.62 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 382 HIS 0.005 0.001 HIS H 518 PHE 0.023 0.002 PHE E 424 TYR 0.013 0.001 TYR D 534 ARG 0.011 0.001 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 11) link_NAG-ASN : angle 5.24114 ( 33) hydrogen bonds : bond 0.03266 ( 532) hydrogen bonds : angle 5.26759 ( 1494) SS BOND : bond 0.00420 ( 28) SS BOND : angle 1.43813 ( 56) covalent geometry : bond 0.00429 (19802) covalent geometry : angle 0.66322 (27093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14194.68 seconds wall clock time: 249 minutes 38.18 seconds (14978.18 seconds total)