Starting phenix.real_space_refine on Wed Oct 28 11:25:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.map" model { file = "/net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ody_20024/10_2026/6ody_20024.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.916 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 54 5.16 5 C 17376 2.51 5 N 5106 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28116 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Chain: "B" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Chain: "C" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Chain: "D" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Chain: "E" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Chain: "F" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4686 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 10, 'TRANS': 682} Chain breaks: 2 Unresolved non-hydrogen bonds: 442 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 221 Planarities with less than four sites: {'UNK:plan-1': 221} Unresolved non-hydrogen planarities: 221 Time building chain proxies: 6.11, per 1000 atoms: 0.22 Number of scatterers: 28116 At special positions: 0 Unit cell: (301.25, 293.75, 68.75, 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 54 16.00 O 5580 8.00 N 5106 7.00 C 17376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.08 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.08 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.08 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.08 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.08 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 947.4 milliseconds 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7716 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 76 sheets defined 8.3% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 705 through 710 removed outlier: 3.561A pdb=" N THR A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 709 " --> pdb=" O VAL A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 removed outlier: 3.547A pdb=" N PHE A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.690A pdb=" N GLY A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 705 through 710 removed outlier: 3.562A pdb=" N THR B 708 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 709 " --> pdb=" O VAL B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 removed outlier: 3.546A pdb=" N PHE B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 754 removed outlier: 3.689A pdb=" N GLY B 754 " --> pdb=" O GLY B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.561A pdb=" N THR C 708 " --> pdb=" O ASN C 705 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C 709 " --> pdb=" O VAL C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 removed outlier: 3.546A pdb=" N PHE C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.691A pdb=" N GLY C 754 " --> pdb=" O GLY C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 Processing helix chain 'D' and resid 79 through 85 Processing helix chain 'D' and resid 705 through 710 removed outlier: 3.562A pdb=" N THR D 708 " --> pdb=" O ASN D 705 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY D 709 " --> pdb=" O VAL D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 removed outlier: 3.547A pdb=" N PHE D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 754 removed outlier: 3.690A pdb=" N GLY D 754 " --> pdb=" O GLY D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 759 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'E' and resid 705 through 710 removed outlier: 3.561A pdb=" N THR E 708 " --> pdb=" O ASN E 705 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY E 709 " --> pdb=" O VAL E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 725 removed outlier: 3.547A pdb=" N PHE E 722 " --> pdb=" O LEU E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 754 removed outlier: 3.690A pdb=" N GLY E 754 " --> pdb=" O GLY E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 759 Processing helix chain 'F' and resid 79 through 85 Processing helix chain 'F' and resid 705 through 710 removed outlier: 3.561A pdb=" N THR F 708 " --> pdb=" O ASN F 705 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F 709 " --> pdb=" O VAL F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 725 removed outlier: 3.546A pdb=" N PHE F 722 " --> pdb=" O LEU F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 754 removed outlier: 3.689A pdb=" N GLY F 754 " --> pdb=" O GLY F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 759 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 removed outlier: 7.651A pdb=" N UNK A 164 " --> pdb=" O UNK A 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 204 removed outlier: 8.112A pdb=" N UNK A 203 " --> pdb=" O UNK A 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N UNK A 227 " --> pdb=" O UNK A 203 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK A 252 " --> pdb=" O UNK A 224 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK A 253 " --> pdb=" O UNK A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 286 removed outlier: 6.533A pdb=" N UNK A 285 " --> pdb=" O ASN A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 293 removed outlier: 6.080A pdb=" N UNK A 292 " --> pdb=" O THR A 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 5.762A pdb=" N VAL A 357 " --> pdb=" O ASN A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 408 removed outlier: 5.971A pdb=" N LEU A 404 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS A 440 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 406 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS A 465 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP A 467 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 439 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 485 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN A 484 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA A 508 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 486 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA A 450 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 471 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 498 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE A 456 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA A 450 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 471 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 498 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS A 494 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N ILE A 514 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN A 496 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU A 516 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN A 498 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 518 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE A 512 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASN A 543 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE A 514 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 545 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLU A 516 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR A 544 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 572 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 546 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A 574 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N LYS A 593 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP A 570 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA A 595 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER A 596 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY A 557 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP A 581 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL A 559 " --> pdb=" O ASP A 581 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 583 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE A 561 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE A 585 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 608 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA A 582 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 610 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN A 584 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN A 612 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS A 586 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 614 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 608 " --> pdb=" O THR A 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 635 through 636 removed outlier: 5.950A pdb=" N ALA A 660 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.684A pdb=" N LEU A 696 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 787 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE A 681 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 729 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'B' and resid 164 through 165 removed outlier: 7.650A pdb=" N UNK B 164 " --> pdb=" O UNK B 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 204 removed outlier: 8.111A pdb=" N UNK B 203 " --> pdb=" O UNK B 225 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N UNK B 227 " --> pdb=" O UNK B 203 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK B 252 " --> pdb=" O UNK B 224 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK B 253 " --> pdb=" O UNK B 273 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 285 through 286 removed outlier: 6.534A pdb=" N UNK B 285 " --> pdb=" O ASN B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 357 through 359 removed outlier: 5.764A pdb=" N VAL B 357 " --> pdb=" O ASN B 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 404 through 408 removed outlier: 5.970A pdb=" N LEU B 404 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS B 440 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 406 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS B 465 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP B 467 " --> pdb=" O PHE B 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE B 439 " --> pdb=" O ASP B 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 485 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN B 484 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA B 508 " --> pdb=" O ASN B 484 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU B 486 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.131A pdb=" N ALA B 450 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 471 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN B 498 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE B 456 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.131A pdb=" N ALA B 450 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 471 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN B 498 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS B 494 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ILE B 514 " --> pdb=" O LYS B 494 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ASN B 496 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLU B 516 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN B 498 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 518 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE B 512 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN B 543 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE B 514 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 545 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLU B 516 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 544 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE B 572 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 546 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 574 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N LYS B 593 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP B 570 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA B 595 " --> pdb=" O ASP B 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER B 596 " --> pdb=" O ASP B 622 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY B 557 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP B 581 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 559 " --> pdb=" O ASP B 581 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 583 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE B 561 " --> pdb=" O ARG B 583 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE B 585 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU B 608 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA B 582 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE B 610 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN B 584 " --> pdb=" O PHE B 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN B 612 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS B 586 " --> pdb=" O ASN B 612 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR B 614 " --> pdb=" O LYS B 586 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B 608 " --> pdb=" O THR B 630 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 635 through 636 removed outlier: 5.949A pdb=" N ALA B 660 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.685A pdb=" N LEU B 696 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 787 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE B 681 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 729 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 127 through 128 Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 165 removed outlier: 7.651A pdb=" N UNK C 164 " --> pdb=" O UNK C 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 203 through 204 removed outlier: 8.112A pdb=" N UNK C 203 " --> pdb=" O UNK C 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N UNK C 227 " --> pdb=" O UNK C 203 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK C 252 " --> pdb=" O UNK C 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK C 253 " --> pdb=" O UNK C 273 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 285 through 286 removed outlier: 6.534A pdb=" N UNK C 285 " --> pdb=" O ASN C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 291 through 293 removed outlier: 6.081A pdb=" N UNK C 292 " --> pdb=" O THR C 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 357 through 359 removed outlier: 5.763A pdb=" N VAL C 357 " --> pdb=" O ASN C 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 404 through 408 removed outlier: 5.971A pdb=" N LEU C 404 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS C 440 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL C 406 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LYS C 465 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE C 437 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP C 467 " --> pdb=" O PHE C 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 439 " --> pdb=" O ASP C 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 485 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN C 484 " --> pdb=" O ASN C 506 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA C 508 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU C 486 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA C 450 " --> pdb=" O ASN C 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 471 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN C 498 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 456 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA C 450 " --> pdb=" O ASN C 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 471 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN C 498 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LYS C 494 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ILE C 514 " --> pdb=" O LYS C 494 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ASN C 496 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLU C 516 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN C 498 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 518 " --> pdb=" O ASN C 498 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE C 512 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN C 543 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE C 514 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL C 545 " --> pdb=" O ILE C 514 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLU C 516 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR C 544 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE C 572 " --> pdb=" O THR C 544 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG C 546 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR C 574 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N LYS C 593 " --> pdb=" O VAL C 568 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP C 570 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA C 595 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER C 596 " --> pdb=" O ASP C 622 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY C 557 " --> pdb=" O TYR C 579 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP C 581 " --> pdb=" O GLY C 557 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL C 559 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 583 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE C 561 " --> pdb=" O ARG C 583 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE C 585 " --> pdb=" O PHE C 561 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 608 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA C 582 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 610 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN C 584 " --> pdb=" O PHE C 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN C 612 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS C 586 " --> pdb=" O ASN C 612 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C 614 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU C 608 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 635 through 636 removed outlier: 5.949A pdb=" N ALA C 660 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.685A pdb=" N LEU C 696 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 787 " --> pdb=" O LEU C 696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE C 681 " --> pdb=" O ALA C 727 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR C 729 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AE4, first strand: chain 'D' and resid 164 through 165 removed outlier: 7.651A pdb=" N UNK D 164 " --> pdb=" O UNK D 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 203 through 204 removed outlier: 8.111A pdb=" N UNK D 203 " --> pdb=" O UNK D 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N UNK D 227 " --> pdb=" O UNK D 203 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N UNK D 252 " --> pdb=" O UNK D 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK D 253 " --> pdb=" O UNK D 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 285 through 286 removed outlier: 6.533A pdb=" N UNK D 285 " --> pdb=" O ASN D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 291 through 293 removed outlier: 6.080A pdb=" N UNK D 292 " --> pdb=" O THR D 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 357 through 359 removed outlier: 5.763A pdb=" N VAL D 357 " --> pdb=" O ASN D 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 404 through 408 removed outlier: 5.971A pdb=" N LEU D 404 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS D 440 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL D 406 " --> pdb=" O LYS D 440 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS D 465 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE D 437 " --> pdb=" O LYS D 465 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP D 467 " --> pdb=" O PHE D 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE D 439 " --> pdb=" O ASP D 467 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 485 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN D 484 " --> pdb=" O ASN D 506 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA D 508 " --> pdb=" O ASN D 484 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 486 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA D 450 " --> pdb=" O ASN D 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 471 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN D 498 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE D 456 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA D 450 " --> pdb=" O ASN D 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 471 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN D 498 " --> pdb=" O ALA D 471 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LYS D 494 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N ILE D 514 " --> pdb=" O LYS D 494 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N ASN D 496 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU D 516 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN D 498 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 518 " --> pdb=" O ASN D 498 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE D 512 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN D 543 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE D 514 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL D 545 " --> pdb=" O ILE D 514 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLU D 516 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR D 544 " --> pdb=" O ASP D 570 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE D 572 " --> pdb=" O THR D 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG D 546 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR D 574 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N LYS D 593 " --> pdb=" O VAL D 568 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP D 570 " --> pdb=" O LYS D 593 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA D 595 " --> pdb=" O ASP D 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER D 596 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY D 557 " --> pdb=" O TYR D 579 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP D 581 " --> pdb=" O GLY D 557 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL D 559 " --> pdb=" O ASP D 581 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG D 583 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE D 561 " --> pdb=" O ARG D 583 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE D 585 " --> pdb=" O PHE D 561 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU D 608 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA D 582 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 610 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN D 584 " --> pdb=" O PHE D 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN D 612 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS D 586 " --> pdb=" O ASN D 612 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 614 " --> pdb=" O LYS D 586 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 608 " --> pdb=" O THR D 630 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 635 through 636 removed outlier: 5.949A pdb=" N ALA D 660 " --> pdb=" O GLY D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.685A pdb=" N LEU D 696 " --> pdb=" O ILE D 787 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 787 " --> pdb=" O LEU D 696 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE D 681 " --> pdb=" O ALA D 727 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR D 729 " --> pdb=" O ILE D 681 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AF8, first strand: chain 'E' and resid 164 through 165 removed outlier: 7.651A pdb=" N UNK E 164 " --> pdb=" O UNK E 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 203 through 204 removed outlier: 8.111A pdb=" N UNK E 203 " --> pdb=" O UNK E 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N UNK E 227 " --> pdb=" O UNK E 203 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK E 252 " --> pdb=" O UNK E 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK E 253 " --> pdb=" O UNK E 273 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 285 through 286 removed outlier: 6.533A pdb=" N UNK E 285 " --> pdb=" O ASN E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'E' and resid 291 through 293 removed outlier: 6.080A pdb=" N UNK E 292 " --> pdb=" O THR E 380 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'E' and resid 357 through 359 removed outlier: 5.763A pdb=" N VAL E 357 " --> pdb=" O ASN E 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'E' and resid 404 through 408 removed outlier: 5.970A pdb=" N LEU E 404 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS E 440 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL E 406 " --> pdb=" O LYS E 440 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS E 465 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE E 437 " --> pdb=" O LYS E 465 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP E 467 " --> pdb=" O PHE E 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE E 439 " --> pdb=" O ASP E 467 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 485 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ASN E 484 " --> pdb=" O ASN E 506 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA E 508 " --> pdb=" O ASN E 484 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU E 486 " --> pdb=" O ALA E 508 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA E 450 " --> pdb=" O ASN E 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 471 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN E 498 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE E 456 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA E 450 " --> pdb=" O ASN E 472 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 471 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN E 498 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS E 494 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N ILE E 514 " --> pdb=" O LYS E 494 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N ASN E 496 " --> pdb=" O ILE E 514 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLU E 516 " --> pdb=" O ASN E 496 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN E 498 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 518 " --> pdb=" O ASN E 498 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE E 512 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN E 543 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE E 514 " --> pdb=" O ASN E 543 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL E 545 " --> pdb=" O ILE E 514 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLU E 516 " --> pdb=" O VAL E 545 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR E 544 " --> pdb=" O ASP E 570 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE E 572 " --> pdb=" O THR E 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG E 546 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR E 574 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N LYS E 593 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP E 570 " --> pdb=" O LYS E 593 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA E 595 " --> pdb=" O ASP E 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER E 596 " --> pdb=" O ASP E 622 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY E 557 " --> pdb=" O TYR E 579 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP E 581 " --> pdb=" O GLY E 557 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL E 559 " --> pdb=" O ASP E 581 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG E 583 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE E 561 " --> pdb=" O ARG E 583 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE E 585 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU E 608 " --> pdb=" O PHE E 580 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA E 582 " --> pdb=" O LEU E 608 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE E 610 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASN E 584 " --> pdb=" O PHE E 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN E 612 " --> pdb=" O ASN E 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS E 586 " --> pdb=" O ASN E 612 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR E 614 " --> pdb=" O LYS E 586 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU E 608 " --> pdb=" O THR E 630 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 635 through 636 removed outlier: 5.949A pdb=" N ALA E 660 " --> pdb=" O GLY E 702 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.684A pdb=" N LEU E 696 " --> pdb=" O ILE E 787 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 787 " --> pdb=" O LEU E 696 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE E 681 " --> pdb=" O ALA E 727 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR E 729 " --> pdb=" O ILE E 681 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AH3, first strand: chain 'F' and resid 164 through 165 removed outlier: 7.650A pdb=" N UNK F 164 " --> pdb=" O UNK F 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'F' and resid 203 through 204 removed outlier: 8.112A pdb=" N UNK F 203 " --> pdb=" O UNK F 225 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N UNK F 227 " --> pdb=" O UNK F 203 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N UNK F 252 " --> pdb=" O UNK F 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N UNK F 253 " --> pdb=" O UNK F 273 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 285 through 286 removed outlier: 6.533A pdb=" N UNK F 285 " --> pdb=" O ASN F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'F' and resid 357 through 359 removed outlier: 5.763A pdb=" N VAL F 357 " --> pdb=" O ASN F 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'F' and resid 404 through 408 removed outlier: 5.970A pdb=" N LEU F 404 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS F 440 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL F 406 " --> pdb=" O LYS F 440 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LYS F 465 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE F 437 " --> pdb=" O LYS F 465 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP F 467 " --> pdb=" O PHE F 437 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE F 439 " --> pdb=" O ASP F 467 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR F 485 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASN F 484 " --> pdb=" O ASN F 506 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ALA F 508 " --> pdb=" O ASN F 484 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU F 486 " --> pdb=" O ALA F 508 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA F 450 " --> pdb=" O ASN F 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 471 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN F 498 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE F 456 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 413 through 415 removed outlier: 6.132A pdb=" N ALA F 450 " --> pdb=" O ASN F 472 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 471 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN F 498 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS F 494 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ILE F 514 " --> pdb=" O LYS F 494 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ASN F 496 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N GLU F 516 " --> pdb=" O ASN F 496 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN F 498 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE F 518 " --> pdb=" O ASN F 498 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE F 512 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN F 543 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE F 514 " --> pdb=" O ASN F 543 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL F 545 " --> pdb=" O ILE F 514 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLU F 516 " --> pdb=" O VAL F 545 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR F 544 " --> pdb=" O ASP F 570 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE F 572 " --> pdb=" O THR F 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG F 546 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR F 574 " --> pdb=" O ARG F 546 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N LYS F 593 " --> pdb=" O VAL F 568 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP F 570 " --> pdb=" O LYS F 593 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA F 595 " --> pdb=" O ASP F 570 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER F 596 " --> pdb=" O ASP F 622 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 530 through 532 removed outlier: 6.973A pdb=" N GLY F 557 " --> pdb=" O TYR F 579 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP F 581 " --> pdb=" O GLY F 557 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL F 559 " --> pdb=" O ASP F 581 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG F 583 " --> pdb=" O VAL F 559 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE F 561 " --> pdb=" O ARG F 583 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE F 585 " --> pdb=" O PHE F 561 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU F 608 " --> pdb=" O PHE F 580 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA F 582 " --> pdb=" O LEU F 608 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE F 610 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN F 584 " --> pdb=" O PHE F 610 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN F 612 " --> pdb=" O ASN F 584 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS F 586 " --> pdb=" O ASN F 612 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR F 614 " --> pdb=" O LYS F 586 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU F 608 " --> pdb=" O THR F 630 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 635 through 636 removed outlier: 5.949A pdb=" N ALA F 660 " --> pdb=" O GLY F 702 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.684A pdb=" N LEU F 696 " --> pdb=" O ILE F 787 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 787 " --> pdb=" O LEU F 696 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 680 through 681 removed outlier: 4.075A pdb=" N ILE F 681 " --> pdb=" O ALA F 727 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR F 729 " --> pdb=" O ILE F 681 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 702 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: 7.26 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 9934 1.35 - 1.48: 6627 1.48 - 1.61: 11777 1.61 - 1.75: 0 1.75 - 1.88: 96 Bond restraints: 28434 Sorted by residual: bond pdb=" N ALA E 377 " pdb=" CA ALA E 377 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N ALA B 377 " pdb=" CA ALA B 377 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.65e+00 bond pdb=" N ALA F 377 " pdb=" CA ALA F 377 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.86e+00 bond pdb=" N ALA D 377 " pdb=" CA ALA D 377 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.64e+00 bond pdb=" N ALA A 377 " pdb=" CA ALA A 377 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.84e+00 ... (remaining 28429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.47: 38651 7.47 - 14.94: 119 14.94 - 22.40: 14 22.40 - 29.87: 7 29.87 - 37.34: 5 Bond angle restraints: 38796 Sorted by residual: angle pdb=" N LYS E 376 " pdb=" CA LYS E 376 " pdb=" C LYS E 376 " ideal model delta sigma weight residual 110.97 145.15 -34.18 1.09e+00 8.42e-01 9.83e+02 angle pdb=" C LEU F 379 " pdb=" CA LEU F 379 " pdb=" CB LEU F 379 " ideal model delta sigma weight residual 116.63 151.94 -35.31 1.16e+00 7.43e-01 9.27e+02 angle pdb=" N LYS B 376 " pdb=" CA LYS B 376 " pdb=" C LYS B 376 " ideal model delta sigma weight residual 110.97 143.60 -32.63 1.09e+00 8.42e-01 8.96e+02 angle pdb=" N LYS F 376 " pdb=" CA LYS F 376 " pdb=" C LYS F 376 " ideal model delta sigma weight residual 111.14 139.53 -28.39 1.08e+00 8.57e-01 6.91e+02 angle pdb=" N LYS D 376 " pdb=" CA LYS D 376 " pdb=" C LYS D 376 " ideal model delta sigma weight residual 110.97 138.84 -27.87 1.09e+00 8.42e-01 6.54e+02 ... (remaining 38791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 14287 15.24 - 30.48: 2061 30.48 - 45.72: 454 45.72 - 60.96: 64 60.96 - 76.20: 24 Dihedral angle restraints: 16890 sinusoidal: 4950 harmonic: 11940 Sorted by residual: dihedral pdb=" C LYS B 376 " pdb=" N LYS B 376 " pdb=" CA LYS B 376 " pdb=" CB LYS B 376 " ideal model delta harmonic sigma weight residual -122.60 -178.63 56.03 0 2.50e+00 1.60e-01 5.02e+02 dihedral pdb=" N LYS B 376 " pdb=" C LYS B 376 " pdb=" CA LYS B 376 " pdb=" CB LYS B 376 " ideal model delta harmonic sigma weight residual 122.80 178.67 -55.87 0 2.50e+00 1.60e-01 4.99e+02 dihedral pdb=" C LYS D 376 " pdb=" N LYS D 376 " pdb=" CA LYS D 376 " pdb=" CB LYS D 376 " ideal model delta harmonic sigma weight residual -122.60 -177.49 54.89 0 2.50e+00 1.60e-01 4.82e+02 ... (remaining 16887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.493: 4695 0.493 - 0.986: 9 0.986 - 1.479: 0 1.479 - 1.972: 0 1.972 - 2.465: 6 Chirality restraints: 4710 Sorted by residual: chirality pdb=" CA LYS B 376 " pdb=" N LYS B 376 " pdb=" C LYS B 376 " pdb=" CB LYS B 376 " both_signs ideal model delta sigma weight residual False 2.51 0.05 2.46 2.00e-01 2.50e+01 1.52e+02 chirality pdb=" CA LYS D 376 " pdb=" N LYS D 376 " pdb=" C LYS D 376 " pdb=" CB LYS D 376 " both_signs ideal model delta sigma weight residual False 2.51 0.09 2.42 2.00e-01 2.50e+01 1.46e+02 chirality pdb=" CA LYS E 376 " pdb=" N LYS E 376 " pdb=" C LYS E 376 " pdb=" CB LYS E 376 " both_signs ideal model delta sigma weight residual False 2.51 0.15 2.36 2.00e-01 2.50e+01 1.40e+02 ... (remaining 4707 not shown) Planarity restraints: 5214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 376 " -0.053 2.00e-02 2.50e+03 1.06e-01 1.13e+02 pdb=" C LYS B 376 " 0.184 2.00e-02 2.50e+03 pdb=" O LYS B 376 " -0.070 2.00e-02 2.50e+03 pdb=" N ALA B 377 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 376 " 0.026 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C LYS E 376 " -0.086 2.00e-02 2.50e+03 pdb=" O LYS E 376 " 0.031 2.00e-02 2.50e+03 pdb=" N ALA E 377 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 376 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LYS A 376 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS A 376 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 377 " -0.023 2.00e-02 2.50e+03 ... (remaining 5211 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 11 1.99 - 2.72: 2877 2.72 - 3.45: 41187 3.45 - 4.17: 68088 4.17 - 4.90: 114860 Nonbonded interactions: 227023 Sorted by model distance: nonbonded pdb=" CB UNK B 291 " pdb=" OG SER B 378 " model vdw 1.264 3.440 nonbonded pdb=" CB UNK C 291 " pdb=" OG SER C 378 " model vdw 1.289 3.440 nonbonded pdb=" CB UNK E 291 " pdb=" OG SER E 378 " model vdw 1.348 3.440 nonbonded pdb=" CA UNK B 291 " pdb=" OG SER B 378 " model vdw 1.734 3.470 nonbonded pdb=" CA UNK C 291 " pdb=" OG SER C 378 " model vdw 1.741 3.470 ... (remaining 227018 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.760 Find NCS groups from input model: 0.210 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 : 0.010 0.071 28440 Z= 0.484 Angle : 1.593 37.341 38808 Z= 0.872 Chirality : 0.111 2.465 4710 Planarity : 0.007 0.106 5214 Dihedral : 15.378 76.201 9156 Min Nonbonded Distance : 1.264 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.63 % Favored : 83.33 % Rotamer: Outliers : 3.15 % Allowed : 13.56 % Favored : 83.29 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.87 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.12), residues: 2820 helix: -4.35 (0.16), residues: 192 sheet: -2.21 (0.20), residues: 606 loop : -3.91 (0.10), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 592 TYR 0.036 0.005 TYR E 579 PHE 0.034 0.005 PHE E 635 TRP 0.018 0.004 TRP B 577 HIS 0.009 0.004 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.48 (28434) covalent geometry : angle 1.59052 / 0.87 (38796) SS BOND : bond 0.04454 / 2.43 ( 6) SS BOND : angle 5.26457 / 2.64 ( 12) hydrogen bonds : bond 0.30529 / 16.73 ( 264) hydrogen bonds : angle 11.98519 / 6.01 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 274 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 LYS cc_start: 0.8799 (mttp) cc_final: 0.8459 (mtmm) REVERT: A 676 LYS cc_start: 0.6103 (mttt) cc_final: 0.5433 (mttm) REVERT: A 692 GLU cc_start: 0.7506 (tt0) cc_final: 0.6662 (pp20) REVERT: B 567 LEU cc_start: 0.6987 (tp) cc_final: 0.6769 (tp) REVERT: B 586 LYS cc_start: 0.8942 (mttp) cc_final: 0.8544 (mtmm) REVERT: B 603 TRP cc_start: 0.2508 (p-90) cc_final: 0.2105 (p-90) REVERT: B 663 MET cc_start: 0.7495 (mmt) cc_final: 0.7170 (mmt) REVERT: B 692 GLU cc_start: 0.7309 (tt0) cc_final: 0.7067 (pp20) REVERT: B 728 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5822 (mt) REVERT: C 692 GLU cc_start: 0.7285 (tt0) cc_final: 0.6725 (pp20) REVERT: C 723 LYS cc_start: 0.5774 (mttt) cc_final: 0.5471 (mttm) REVERT: D 586 LYS cc_start: 0.8734 (mttp) cc_final: 0.8417 (mtmm) REVERT: D 676 LYS cc_start: 0.6210 (mttt) cc_final: 0.5534 (mttm) REVERT: D 692 GLU cc_start: 0.7513 (tt0) cc_final: 0.6676 (pp20) REVERT: D 766 LYS cc_start: 0.3829 (mtpt) cc_final: 0.3619 (mtpt) REVERT: E 567 LEU cc_start: 0.7134 (tp) cc_final: 0.6912 (tp) REVERT: E 586 LYS cc_start: 0.8905 (mttp) cc_final: 0.8529 (mtmm) REVERT: E 603 TRP cc_start: 0.2659 (p-90) cc_final: 0.2222 (p-90) REVERT: E 663 MET cc_start: 0.7489 (mmt) cc_final: 0.7235 (mmt) REVERT: E 692 GLU cc_start: 0.7277 (tt0) cc_final: 0.7021 (pp20) REVERT: E 728 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5842 (mp) REVERT: F 692 GLU cc_start: 0.7305 (tt0) cc_final: 0.6761 (pp20) REVERT: F 723 LYS cc_start: 0.5597 (mttt) cc_final: 0.5303 (mttm) outliers start: 74 outliers final: 32 residues processed: 334 average time/residue: 0.1874 time to fit residues: 95.9943 Evaluate side-chains 225 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 376 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 728 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 746 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN A 398 GLN A 472 ASN A 484 ASN A 498 ASN A 515 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN A 632 GLN A 643 ASN A 732 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 387 ASN B 398 GLN B 453 ASN B 472 ASN B 484 ASN B 498 ASN B 515 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 628 ASN B 643 ASN B 732 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 398 GLN C 453 ASN C 472 ASN C 484 ASN C 498 ASN C 515 ASN ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 628 ASN C 643 ASN C 731 ASN C 732 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN D 398 GLN D 472 ASN D 484 ASN D 498 ASN D 515 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN D 632 GLN D 643 ASN D 732 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 387 ASN E 398 GLN E 453 ASN E 472 ASN E 484 ASN E 498 ASN E 515 ASN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 ASN E 643 ASN E 732 ASN ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN F 398 GLN F 453 ASN F 472 ASN F 484 ASN F 498 ASN F 515 ASN ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN F 628 ASN F 643 ASN F 731 ASN F 732 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.099673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.090018 restraints weight = 137624.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089764 restraints weight = 130680.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089733 restraints weight = 135291.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.089865 restraints weight = 125623.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.089908 restraints weight = 109601.395| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 28440 Z= 0.341 Angle : 1.217 13.533 38808 Z= 0.575 Chirality : 0.058 0.269 4710 Planarity : 0.005 0.047 5214 Dihedral : 9.473 50.314 4350 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.29 % Favored : 85.67 % Rotamer: Outliers : 7.10 % Allowed : 19.01 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.13), residues: 2820 helix: -3.70 (0.23), residues: 192 sheet: -2.84 (0.17), residues: 810 loop : -3.70 (0.12), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 741 TYR 0.031 0.003 TYR C 791 PHE 0.029 0.003 PHE A 635 TRP 0.020 0.003 TRP C 603 HIS 0.005 0.002 HIS F 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.34 (28434) covalent geometry : angle 1.21590 / 0.57 (38796) SS BOND : bond 0.03081 / 1.69 ( 6) SS BOND : angle 3.01527 / 1.51 ( 12) hydrogen bonds : bond 0.05092 / 2.80 ( 264) hydrogen bonds : angle 7.75041 / 3.90 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 191 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.5352 (p90) REVERT: A 586 LYS cc_start: 0.8761 (mttp) cc_final: 0.8479 (mtmm) REVERT: A 687 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3809 (mm) REVERT: A 692 GLU cc_start: 0.7373 (tt0) cc_final: 0.6396 (mm-30) REVERT: A 789 VAL cc_start: 0.6026 (OUTLIER) cc_final: 0.5116 (p) REVERT: B 567 LEU cc_start: 0.7083 (tp) cc_final: 0.6879 (tp) REVERT: B 586 LYS cc_start: 0.8767 (mttp) cc_final: 0.8462 (mtmm) REVERT: B 603 TRP cc_start: 0.2672 (p-90) cc_final: 0.2382 (p-90) REVERT: B 663 MET cc_start: 0.6983 (mmt) cc_final: 0.6434 (mmt) REVERT: B 687 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3769 (mm) REVERT: B 692 GLU cc_start: 0.7498 (tt0) cc_final: 0.6704 (pp20) REVERT: C 692 GLU cc_start: 0.6767 (tt0) cc_final: 0.6318 (pp20) REVERT: D 586 LYS cc_start: 0.8731 (mttp) cc_final: 0.8445 (mtmm) REVERT: D 687 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3817 (mm) REVERT: D 692 GLU cc_start: 0.7385 (tt0) cc_final: 0.6401 (mm-30) REVERT: D 789 VAL cc_start: 0.6053 (OUTLIER) cc_final: 0.5137 (p) REVERT: E 567 LEU cc_start: 0.7075 (tp) cc_final: 0.6860 (tp) REVERT: E 586 LYS cc_start: 0.8749 (mttp) cc_final: 0.8447 (mtmm) REVERT: E 603 TRP cc_start: 0.2672 (p-90) cc_final: 0.2387 (p-90) REVERT: E 663 MET cc_start: 0.7077 (mmt) cc_final: 0.6525 (mmt) REVERT: E 687 LEU cc_start: 0.3995 (OUTLIER) cc_final: 0.3784 (mm) REVERT: E 692 GLU cc_start: 0.7527 (tt0) cc_final: 0.6726 (pp20) REVERT: F 662 MET cc_start: 0.6823 (mmm) cc_final: 0.6581 (mmm) REVERT: F 692 GLU cc_start: 0.6835 (tt0) cc_final: 0.6357 (pp20) outliers start: 167 outliers final: 104 residues processed: 345 average time/residue: 0.1569 time to fit residues: 89.1025 Evaluate side-chains 286 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 175 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 552 ARG Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 740 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 398 GLN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS B 398 GLN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 GLN C 731 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 HIS D 398 GLN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 HIS E 398 GLN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.117431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.104557 restraints weight = 143535.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.104273 restraints weight = 105670.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.104590 restraints weight = 93395.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.104679 restraints weight = 82723.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.104716 restraints weight = 79625.499| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28440 Z= 0.332 Angle : 1.195 13.739 38808 Z= 0.567 Chirality : 0.058 0.279 4710 Planarity : 0.006 0.079 5214 Dihedral : 9.244 48.307 4338 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.49 % Favored : 83.48 % Rotamer: Outliers : 8.29 % Allowed : 22.79 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.13), residues: 2820 helix: -3.12 (0.32), residues: 156 sheet: -2.46 (0.20), residues: 606 loop : -3.73 (0.11), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 741 TYR 0.030 0.003 TYR F 791 PHE 0.028 0.003 PHE D 635 TRP 0.016 0.002 TRP F 577 HIS 0.005 0.002 HIS B 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.33 (28434) covalent geometry : angle 1.19369 / 0.57 (38796) SS BOND : bond 0.03091 / 1.69 ( 6) SS BOND : angle 3.02588 / 1.52 ( 12) hydrogen bonds : bond 0.05144 / 2.82 ( 264) hydrogen bonds : angle 7.52725 / 3.80 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 192 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 LYS cc_start: 0.8961 (mttp) cc_final: 0.8633 (mtmm) REVERT: A 589 GLU cc_start: 0.7231 (tt0) cc_final: 0.6636 (tp30) REVERT: A 666 ASN cc_start: 0.3098 (OUTLIER) cc_final: 0.2717 (t0) REVERT: A 676 LYS cc_start: 0.6140 (mttt) cc_final: 0.5502 (mttm) REVERT: A 687 LEU cc_start: 0.4255 (OUTLIER) cc_final: 0.3811 (mm) REVERT: A 692 GLU cc_start: 0.7287 (tt0) cc_final: 0.6402 (mm-30) REVERT: A 789 VAL cc_start: 0.6121 (OUTLIER) cc_final: 0.5358 (p) REVERT: B 354 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: B 567 LEU cc_start: 0.7485 (tp) cc_final: 0.7199 (tp) REVERT: B 572 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7401 (t80) REVERT: B 586 LYS cc_start: 0.9021 (mttp) cc_final: 0.8625 (mtmm) REVERT: B 603 TRP cc_start: 0.3262 (p-90) cc_final: 0.3023 (p-90) REVERT: B 663 MET cc_start: 0.7217 (mmt) cc_final: 0.6631 (mmt) REVERT: B 692 GLU cc_start: 0.7294 (tt0) cc_final: 0.6579 (pp20) REVERT: C 547 LEU cc_start: 0.5842 (mt) cc_final: 0.5358 (mt) REVERT: C 572 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7524 (t80) REVERT: C 692 GLU cc_start: 0.6703 (tt0) cc_final: 0.6032 (mm-30) REVERT: D 586 LYS cc_start: 0.8958 (mttp) cc_final: 0.8630 (mtmm) REVERT: D 589 GLU cc_start: 0.7226 (tt0) cc_final: 0.6625 (tp30) REVERT: D 676 LYS cc_start: 0.6223 (mttt) cc_final: 0.5561 (mttm) REVERT: D 687 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.3822 (mm) REVERT: D 692 GLU cc_start: 0.7287 (tt0) cc_final: 0.6402 (mm-30) REVERT: D 789 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5371 (p) REVERT: E 354 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: E 567 LEU cc_start: 0.7450 (tp) cc_final: 0.7144 (tp) REVERT: E 572 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7401 (t80) REVERT: E 586 LYS cc_start: 0.9028 (mttp) cc_final: 0.8610 (mtmm) REVERT: E 603 TRP cc_start: 0.3298 (p-90) cc_final: 0.3061 (p-90) REVERT: E 663 MET cc_start: 0.7242 (mmt) cc_final: 0.6657 (mmt) REVERT: E 692 GLU cc_start: 0.7302 (tt0) cc_final: 0.6589 (pp20) REVERT: F 547 LEU cc_start: 0.5825 (mt) cc_final: 0.5353 (mt) REVERT: F 572 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (t80) REVERT: F 662 MET cc_start: 0.7177 (mmm) cc_final: 0.6616 (mmm) REVERT: F 692 GLU cc_start: 0.6704 (tt0) cc_final: 0.6022 (mm-30) outliers start: 195 outliers final: 119 residues processed: 372 average time/residue: 0.1441 time to fit residues: 90.7330 Evaluate side-chains 310 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 180 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 552 ARG Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 646 VAL Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 HIS ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 721 GLN F 731 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.098495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088837 restraints weight = 141450.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.089054 restraints weight = 126041.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.088864 restraints weight = 116524.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.089012 restraints weight = 111058.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.089123 restraints weight = 100169.521| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 28440 Z= 0.329 Angle : 1.180 13.295 38808 Z= 0.563 Chirality : 0.057 0.260 4710 Planarity : 0.006 0.068 5214 Dihedral : 9.201 49.390 4338 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 17.06 % Favored : 82.91 % Rotamer: Outliers : 9.27 % Allowed : 24.40 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.13), residues: 2820 helix: -2.87 (0.35), residues: 156 sheet: -2.38 (0.21), residues: 606 loop : -3.79 (0.11), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 541 TYR 0.029 0.003 TYR A 579 PHE 0.030 0.003 PHE D 635 TRP 0.012 0.002 TRP C 577 HIS 0.004 0.002 HIS C 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.33 (28434) covalent geometry : angle 1.17943 / 0.56 (38796) SS BOND : bond 0.02926 / 1.61 ( 6) SS BOND : angle 2.81589 / 1.41 ( 12) hydrogen bonds : bond 0.04808 / 2.63 ( 264) hydrogen bonds : angle 7.39450 / 3.73 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 186 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 515 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7532 (m-40) REVERT: A 586 LYS cc_start: 0.8701 (mttp) cc_final: 0.8430 (mtmm) REVERT: A 666 ASN cc_start: 0.2593 (OUTLIER) cc_final: 0.2224 (t0) REVERT: A 676 LYS cc_start: 0.6368 (mttt) cc_final: 0.5647 (mttm) REVERT: A 687 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.3620 (mm) REVERT: A 692 GLU cc_start: 0.7684 (tt0) cc_final: 0.6675 (mm-30) REVERT: A 789 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.5706 (p) REVERT: B 586 LYS cc_start: 0.8752 (mttp) cc_final: 0.8422 (mtmm) REVERT: B 594 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7195 (t80) REVERT: B 603 TRP cc_start: 0.2177 (p-90) cc_final: 0.1871 (p-90) REVERT: B 663 MET cc_start: 0.7213 (mmt) cc_final: 0.6607 (mmt) REVERT: C 343 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: C 509 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8082 (t) REVERT: C 515 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: C 621 MET cc_start: 0.6830 (mpp) cc_final: 0.6616 (mpp) REVERT: C 692 GLU cc_start: 0.6547 (tt0) cc_final: 0.6191 (pp20) REVERT: C 760 ASN cc_start: 0.6254 (OUTLIER) cc_final: 0.5914 (t0) REVERT: D 355 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (p) REVERT: D 515 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7534 (m-40) REVERT: D 586 LYS cc_start: 0.8689 (mttp) cc_final: 0.8425 (mtmm) REVERT: D 676 LYS cc_start: 0.6365 (mttt) cc_final: 0.5652 (mttm) REVERT: D 687 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.3627 (mm) REVERT: D 692 GLU cc_start: 0.7678 (tt0) cc_final: 0.6662 (mm-30) REVERT: D 789 VAL cc_start: 0.6329 (OUTLIER) cc_final: 0.5692 (p) REVERT: E 586 LYS cc_start: 0.8765 (mttp) cc_final: 0.8450 (mtmm) REVERT: E 594 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7036 (t80) REVERT: E 603 TRP cc_start: 0.2209 (p-90) cc_final: 0.1891 (p-90) REVERT: E 663 MET cc_start: 0.7256 (mmt) cc_final: 0.6626 (mmt) REVERT: F 343 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: F 509 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8115 (t) REVERT: F 515 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: F 662 MET cc_start: 0.6968 (mmm) cc_final: 0.6532 (mmm) REVERT: F 692 GLU cc_start: 0.6595 (tt0) cc_final: 0.6219 (pp20) REVERT: F 760 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.5904 (t0) outliers start: 218 outliers final: 137 residues processed: 377 average time/residue: 0.1473 time to fit residues: 93.5944 Evaluate side-chains 327 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 171 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 552 ARG Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 ASN ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 775 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 = 0.4113 r_free = 0.4113 target = 0.098368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.088980 restraints weight = 142203.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.089007 restraints weight = 130791.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.088809 restraints weight = 127882.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.088971 restraints weight = 118249.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.089271 restraints weight = 101863.978| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28440 Z= 0.328 Angle : 1.177 11.654 38808 Z= 0.561 Chirality : 0.057 0.203 4710 Planarity : 0.006 0.063 5214 Dihedral : 9.087 56.370 4336 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 17.48 % Favored : 82.48 % Rotamer: Outliers : 10.80 % Allowed : 25.55 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.13), residues: 2820 helix: -2.78 (0.35), residues: 156 sheet: -2.40 (0.20), residues: 594 loop : -3.84 (0.11), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 541 TYR 0.029 0.003 TYR D 579 PHE 0.029 0.003 PHE B 635 TRP 0.011 0.002 TRP C 577 HIS 0.004 0.002 HIS B 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (28434) covalent geometry : angle 1.17643 / 0.56 (38796) SS BOND : bond 0.02985 / 1.63 ( 6) SS BOND : angle 2.97269 / 1.50 ( 12) hydrogen bonds : bond 0.04905 / 2.68 ( 264) hydrogen bonds : angle 7.36830 / 3.72 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 193 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: A 355 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 586 LYS cc_start: 0.8754 (mttp) cc_final: 0.8455 (mtmm) REVERT: A 666 ASN cc_start: 0.2620 (OUTLIER) cc_final: 0.1857 (t0) REVERT: A 675 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.3754 (m-80) REVERT: A 676 LYS cc_start: 0.6063 (mttt) cc_final: 0.5397 (mttm) REVERT: A 687 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3646 (mm) REVERT: A 692 GLU cc_start: 0.7674 (tt0) cc_final: 0.6657 (mm-30) REVERT: A 789 VAL cc_start: 0.6308 (OUTLIER) cc_final: 0.5707 (p) REVERT: B 572 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6433 (t80) REVERT: B 586 LYS cc_start: 0.8724 (mttp) cc_final: 0.8399 (mtmm) REVERT: B 594 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.7122 (t80) REVERT: B 639 GLN cc_start: 0.3051 (pt0) cc_final: 0.2549 (pt0) REVERT: B 663 MET cc_start: 0.7281 (mmt) cc_final: 0.6637 (mmt) REVERT: C 343 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: C 509 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8063 (t) REVERT: C 547 LEU cc_start: 0.5008 (mt) cc_final: 0.4627 (mt) REVERT: C 572 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6990 (t80) REVERT: C 675 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5427 (m-80) REVERT: C 692 GLU cc_start: 0.6531 (tt0) cc_final: 0.6250 (pp20) REVERT: D 355 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7846 (p) REVERT: D 509 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8263 (t) REVERT: D 586 LYS cc_start: 0.8768 (mttp) cc_final: 0.8467 (mtmm) REVERT: D 675 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.3746 (m-80) REVERT: D 676 LYS cc_start: 0.6116 (mttt) cc_final: 0.5430 (mttm) REVERT: D 687 LEU cc_start: 0.4097 (OUTLIER) cc_final: 0.3642 (mm) REVERT: D 692 GLU cc_start: 0.7660 (tt0) cc_final: 0.6637 (mm-30) REVERT: D 789 VAL cc_start: 0.6275 (OUTLIER) cc_final: 0.5662 (p) REVERT: E 515 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7173 (m-40) REVERT: E 572 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6459 (t80) REVERT: E 586 LYS cc_start: 0.8696 (mttp) cc_final: 0.8375 (mtmm) REVERT: E 594 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7144 (t80) REVERT: E 639 GLN cc_start: 0.3415 (pt0) cc_final: 0.2914 (pt0) REVERT: E 663 MET cc_start: 0.7356 (mmt) cc_final: 0.6683 (mmt) REVERT: F 343 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: F 509 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8107 (t) REVERT: F 547 LEU cc_start: 0.4975 (mt) cc_final: 0.4578 (mt) REVERT: F 572 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6993 (t80) REVERT: F 662 MET cc_start: 0.7047 (mmm) cc_final: 0.6721 (mmm) REVERT: F 675 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: F 692 GLU cc_start: 0.6541 (tt0) cc_final: 0.6268 (pp20) outliers start: 254 outliers final: 165 residues processed: 420 average time/residue: 0.1414 time to fit residues: 101.3003 Evaluate side-chains 376 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 187 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 572 PHE Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 552 ARG Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 739 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 572 PHE Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 711 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 760 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 ASN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 ASN ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 760 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.098177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088781 restraints weight = 143471.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088918 restraints weight = 130639.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.088815 restraints weight = 120311.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.088988 restraints weight = 113967.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.089071 restraints weight = 97399.450| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 28440 Z= 0.327 Angle : 1.173 11.636 38808 Z= 0.559 Chirality : 0.057 0.188 4710 Planarity : 0.005 0.061 5214 Dihedral : 9.026 54.911 4334 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.27 % Favored : 82.66 % Rotamer: Outliers : 11.14 % Allowed : 26.66 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.13), residues: 2820 helix: -2.97 (0.29), residues: 198 sheet: -2.46 (0.20), residues: 594 loop : -3.81 (0.11), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 541 TYR 0.030 0.003 TYR D 579 PHE 0.030 0.003 PHE B 635 TRP 0.010 0.002 TRP F 577 HIS 0.006 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (28434) covalent geometry : angle 1.17167 / 0.56 (38796) SS BOND : bond 0.02939 / 1.61 ( 6) SS BOND : angle 2.85757 / 1.44 ( 12) hydrogen bonds : bond 0.04842 / 2.65 ( 264) hydrogen bonds : angle 7.36879 / 3.72 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 184 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: A 355 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 515 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.6682 (t0) REVERT: A 516 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: A 586 LYS cc_start: 0.8773 (mttp) cc_final: 0.8484 (mtmm) REVERT: A 675 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.3790 (m-80) REVERT: A 676 LYS cc_start: 0.6163 (mttt) cc_final: 0.5493 (mttm) REVERT: A 687 LEU cc_start: 0.4578 (OUTLIER) cc_final: 0.4099 (mm) REVERT: A 692 GLU cc_start: 0.7593 (tt0) cc_final: 0.6513 (mm-30) REVERT: A 789 VAL cc_start: 0.6244 (OUTLIER) cc_final: 0.5639 (p) REVERT: B 572 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6354 (t80) REVERT: B 586 LYS cc_start: 0.8694 (mttp) cc_final: 0.8372 (mtmm) REVERT: B 639 GLN cc_start: 0.3222 (pt0) cc_final: 0.2669 (pt0) REVERT: B 663 MET cc_start: 0.7334 (mmt) cc_final: 0.6712 (mmt) REVERT: B 692 GLU cc_start: 0.7394 (tt0) cc_final: 0.6735 (pp20) REVERT: C 343 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: C 509 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8073 (t) REVERT: C 515 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7439 (t0) REVERT: C 675 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.5472 (m-80) REVERT: C 692 GLU cc_start: 0.6718 (tt0) cc_final: 0.6164 (mm-30) REVERT: C 747 LYS cc_start: 0.3462 (mttt) cc_final: 0.3119 (tmtt) REVERT: C 789 VAL cc_start: 0.6446 (OUTLIER) cc_final: 0.6070 (p) REVERT: D 343 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: D 355 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7904 (p) REVERT: D 515 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7189 (t0) REVERT: D 586 LYS cc_start: 0.8805 (mttp) cc_final: 0.8510 (mtmm) REVERT: D 675 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.3711 (m-80) REVERT: D 676 LYS cc_start: 0.6146 (mttt) cc_final: 0.5476 (mttm) REVERT: D 687 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.4111 (mm) REVERT: D 692 GLU cc_start: 0.7570 (tt0) cc_final: 0.6487 (mm-30) REVERT: D 789 VAL cc_start: 0.6201 (OUTLIER) cc_final: 0.5582 (p) REVERT: E 572 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.6419 (t80) REVERT: E 586 LYS cc_start: 0.8698 (mttp) cc_final: 0.8363 (mtmm) REVERT: E 594 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7137 (t80) REVERT: E 663 MET cc_start: 0.7288 (mmt) cc_final: 0.6633 (mmt) REVERT: F 343 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: F 375 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: F 499 LYS cc_start: 0.7336 (tptt) cc_final: 0.6903 (tmtt) REVERT: F 509 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (t) REVERT: F 515 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7437 (t0) REVERT: F 547 LEU cc_start: 0.5091 (mt) cc_final: 0.4752 (mt) REVERT: F 662 MET cc_start: 0.7049 (mmm) cc_final: 0.6742 (mmm) REVERT: F 675 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5689 (m-80) REVERT: F 692 GLU cc_start: 0.6696 (tt0) cc_final: 0.6132 (mm-30) REVERT: F 747 LYS cc_start: 0.3354 (mttt) cc_final: 0.3043 (tmtt) REVERT: F 789 VAL cc_start: 0.6410 (OUTLIER) cc_final: 0.6043 (p) outliers start: 262 outliers final: 191 residues processed: 423 average time/residue: 0.1432 time to fit residues: 102.8507 Evaluate side-chains 393 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 175 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 666 ASN Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 791 TYR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 791 TYR Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 739 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 412 ASN Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 518 ILE Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 789 VAL Chi-restraints excluded: chain F residue 791 TYR Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 760 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 760 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.088317 restraints weight = 143183.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.088658 restraints weight = 130308.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.088719 restraints weight = 108438.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.088830 restraints weight = 104296.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088927 restraints weight = 98275.087| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 28440 Z= 0.327 Angle : 1.169 11.515 38808 Z= 0.558 Chirality : 0.057 0.317 4710 Planarity : 0.005 0.059 5214 Dihedral : 8.996 49.347 4333 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 18.09 % Favored : 81.88 % Rotamer: Outliers : 11.27 % Allowed : 27.13 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.13), residues: 2820 helix: -2.88 (0.30), residues: 198 sheet: -2.44 (0.20), residues: 594 loop : -3.80 (0.11), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 541 TYR 0.030 0.003 TYR A 579 PHE 0.030 0.003 PHE B 635 TRP 0.012 0.002 TRP B 577 HIS 0.006 0.002 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (28434) covalent geometry : angle 1.16763 / 0.56 (38796) SS BOND : bond 0.02955 / 1.62 ( 6) SS BOND : angle 2.98006 / 1.50 ( 12) hydrogen bonds : bond 0.04839 / 2.64 ( 264) hydrogen bonds : angle 7.38528 / 3.73 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 174 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 355 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 515 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.6725 (t0) REVERT: A 586 LYS cc_start: 0.8788 (mttp) cc_final: 0.8496 (mtmm) REVERT: A 675 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.3757 (m-80) REVERT: A 676 LYS cc_start: 0.6225 (mttt) cc_final: 0.5550 (mttm) REVERT: A 687 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4470 (mm) REVERT: A 692 GLU cc_start: 0.7626 (tt0) cc_final: 0.6559 (mm-30) REVERT: A 789 VAL cc_start: 0.6203 (OUTLIER) cc_final: 0.5622 (p) REVERT: B 520 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6969 (tttm) REVERT: B 572 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6441 (t80) REVERT: B 663 MET cc_start: 0.7362 (mmt) cc_final: 0.6739 (mmt) REVERT: B 806 ASN cc_start: 0.2890 (OUTLIER) cc_final: 0.2503 (m-40) REVERT: C 343 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: C 509 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8063 (t) REVERT: C 515 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7429 (t0) REVERT: C 675 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.5645 (m-80) REVERT: C 747 LYS cc_start: 0.3469 (mttt) cc_final: 0.3119 (tmtt) REVERT: D 343 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: D 355 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7967 (p) REVERT: D 515 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7102 (t0) REVERT: D 586 LYS cc_start: 0.8820 (mttp) cc_final: 0.8522 (mtmm) REVERT: D 675 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.3676 (m-80) REVERT: D 676 LYS cc_start: 0.6232 (mttt) cc_final: 0.5544 (mttm) REVERT: D 687 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4476 (mm) REVERT: D 692 GLU cc_start: 0.7614 (tt0) cc_final: 0.6541 (mm-30) REVERT: D 789 VAL cc_start: 0.6176 (OUTLIER) cc_final: 0.5589 (p) REVERT: E 520 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6968 (tttm) REVERT: E 572 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6484 (t80) REVERT: E 594 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7112 (t80) REVERT: E 663 MET cc_start: 0.7346 (mmt) cc_final: 0.6692 (mmt) REVERT: F 343 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: F 375 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: F 509 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8087 (t) REVERT: F 515 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7458 (t0) REVERT: F 662 MET cc_start: 0.7068 (mmm) cc_final: 0.6807 (mmm) REVERT: F 675 TYR cc_start: 0.6157 (OUTLIER) cc_final: 0.5610 (m-80) REVERT: F 692 GLU cc_start: 0.6830 (tt0) cc_final: 0.6317 (mm-30) REVERT: F 747 LYS cc_start: 0.3447 (mttt) cc_final: 0.3098 (tmtt) REVERT: F 789 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6088 (p) outliers start: 265 outliers final: 198 residues processed: 414 average time/residue: 0.1390 time to fit residues: 99.0679 Evaluate side-chains 395 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 169 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 LYS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 791 TYR Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 791 TYR Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 739 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 732 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 789 VAL Chi-restraints excluded: chain F residue 791 TYR Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 760 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 ASN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 760 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.098166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.088589 restraints weight = 143606.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.089035 restraints weight = 128974.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.088972 restraints weight = 111361.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.089154 restraints weight = 101929.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.089168 restraints weight = 87709.040| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 28440 Z= 0.327 Angle : 1.167 11.461 38808 Z= 0.559 Chirality : 0.057 0.280 4710 Planarity : 0.005 0.059 5214 Dihedral : 9.007 50.210 4333 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 17.87 % Favored : 82.09 % Rotamer: Outliers : 11.35 % Allowed : 27.38 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.13), residues: 2820 helix: -2.86 (0.30), residues: 198 sheet: -2.42 (0.20), residues: 594 loop : -3.81 (0.11), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 541 TYR 0.031 0.003 TYR A 579 PHE 0.030 0.003 PHE B 635 TRP 0.013 0.003 TRP B 577 HIS 0.006 0.002 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.33 (28434) covalent geometry : angle 1.16644 / 0.56 (38796) SS BOND : bond 0.02884 / 1.57 ( 6) SS BOND : angle 2.83642 / 1.44 ( 12) hydrogen bonds : bond 0.04847 / 2.66 ( 264) hydrogen bonds : angle 7.39992 / 3.73 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 173 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: A 355 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 515 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7237 (t0) REVERT: A 586 LYS cc_start: 0.8798 (mttp) cc_final: 0.8508 (mtmm) REVERT: A 675 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.3676 (m-80) REVERT: A 676 LYS cc_start: 0.6228 (mttt) cc_final: 0.5536 (mttm) REVERT: A 687 LEU cc_start: 0.5021 (OUTLIER) cc_final: 0.4449 (mm) REVERT: A 692 GLU cc_start: 0.7650 (tt0) cc_final: 0.6580 (mm-30) REVERT: A 789 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5651 (p) REVERT: B 520 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6913 (tttm) REVERT: B 572 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6328 (t80) REVERT: B 663 MET cc_start: 0.7385 (mmt) cc_final: 0.6756 (mmt) REVERT: B 806 ASN cc_start: 0.2804 (OUTLIER) cc_final: 0.2430 (m-40) REVERT: C 343 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: C 509 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8094 (t) REVERT: C 515 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7448 (t0) REVERT: C 675 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: C 747 LYS cc_start: 0.3428 (mttt) cc_final: 0.3067 (tmtt) REVERT: D 343 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: D 355 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7842 (p) REVERT: D 515 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7073 (t0) REVERT: D 586 LYS cc_start: 0.8805 (mttp) cc_final: 0.8513 (mtmm) REVERT: D 675 TYR cc_start: 0.5642 (OUTLIER) cc_final: 0.3640 (m-80) REVERT: D 676 LYS cc_start: 0.6273 (mttt) cc_final: 0.5567 (mttm) REVERT: D 687 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4470 (mm) REVERT: D 692 GLU cc_start: 0.7555 (tt0) cc_final: 0.6446 (mm-30) REVERT: D 789 VAL cc_start: 0.6167 (OUTLIER) cc_final: 0.5563 (p) REVERT: E 520 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6908 (tttm) REVERT: E 572 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6402 (t80) REVERT: E 594 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.7028 (t80) REVERT: E 663 MET cc_start: 0.7356 (mmt) cc_final: 0.6688 (mmt) REVERT: F 343 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: F 509 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8109 (t) REVERT: F 515 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7481 (t0) REVERT: F 662 MET cc_start: 0.7025 (mmm) cc_final: 0.6821 (mmm) REVERT: F 675 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5692 (m-80) REVERT: F 692 GLU cc_start: 0.6800 (tt0) cc_final: 0.6354 (mm-30) REVERT: F 747 LYS cc_start: 0.3423 (mttt) cc_final: 0.3062 (tmtt) REVERT: F 789 VAL cc_start: 0.6427 (OUTLIER) cc_final: 0.6081 (p) outliers start: 267 outliers final: 202 residues processed: 416 average time/residue: 0.1366 time to fit residues: 97.1855 Evaluate side-chains 400 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 171 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 LYS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 731 ASN Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 791 TYR Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 469 HIS Chi-restraints excluded: chain E residue 496 ASN Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 710 THR Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 732 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 789 VAL Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 760 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 760 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN D 760 ASN ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 760 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088454 restraints weight = 142891.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.088937 restraints weight = 123122.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.088921 restraints weight = 103168.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.089173 restraints weight = 94969.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.089161 restraints weight = 85062.970| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 28440 Z= 0.328 Angle : 1.167 11.468 38808 Z= 0.559 Chirality : 0.057 0.265 4710 Planarity : 0.005 0.058 5214 Dihedral : 9.001 49.956 4331 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 18.19 % Favored : 81.77 % Rotamer: Outliers : 10.54 % Allowed : 28.36 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.13), residues: 2820 helix: -2.91 (0.30), residues: 204 sheet: -2.40 (0.20), residues: 594 loop : -3.83 (0.11), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 541 TYR 0.030 0.003 TYR A 579 PHE 0.030 0.003 PHE B 635 TRP 0.010 0.002 TRP F 577 HIS 0.006 0.002 HIS E 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.33 (28434) covalent geometry : angle 1.16626 / 0.56 (38796) SS BOND : bond 0.02920 / 1.59 ( 6) SS BOND : angle 2.86771 / 1.45 ( 12) hydrogen bonds : bond 0.04862 / 2.66 ( 264) hydrogen bonds : angle 7.41221 / 3.73 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 174 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: A 355 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7908 (p) REVERT: A 515 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7236 (t0) REVERT: A 586 LYS cc_start: 0.8818 (mttp) cc_final: 0.8516 (mtmm) REVERT: A 675 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: A 676 LYS cc_start: 0.6235 (mttt) cc_final: 0.5540 (mttm) REVERT: A 687 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4491 (mm) REVERT: A 692 GLU cc_start: 0.7645 (tt0) cc_final: 0.6568 (mm-30) REVERT: A 789 VAL cc_start: 0.6235 (OUTLIER) cc_final: 0.5630 (p) REVERT: B 520 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6909 (tttm) REVERT: B 572 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6358 (t80) REVERT: B 663 MET cc_start: 0.7366 (mmt) cc_final: 0.6746 (mmt) REVERT: B 791 TYR cc_start: 0.4675 (OUTLIER) cc_final: 0.4261 (t80) REVERT: B 806 ASN cc_start: 0.2840 (OUTLIER) cc_final: 0.2441 (m-40) REVERT: C 343 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: C 509 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8106 (t) REVERT: C 515 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7524 (t0) REVERT: C 675 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: C 747 LYS cc_start: 0.3435 (mttt) cc_final: 0.3103 (tmtt) REVERT: D 343 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: D 355 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7884 (p) REVERT: D 515 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7261 (t0) REVERT: D 586 LYS cc_start: 0.8803 (mttp) cc_final: 0.8506 (mtmm) REVERT: D 675 TYR cc_start: 0.5603 (OUTLIER) cc_final: 0.3620 (m-80) REVERT: D 676 LYS cc_start: 0.6226 (mttt) cc_final: 0.5535 (mttm) REVERT: D 687 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4492 (mm) REVERT: D 692 GLU cc_start: 0.7618 (tt0) cc_final: 0.6524 (mm-30) REVERT: D 789 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5550 (p) REVERT: E 520 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6876 (tttm) REVERT: E 572 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.6402 (t80) REVERT: E 594 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7077 (t80) REVERT: E 663 MET cc_start: 0.7348 (mmt) cc_final: 0.6681 (mmt) REVERT: E 791 TYR cc_start: 0.4605 (OUTLIER) cc_final: 0.4206 (t80) REVERT: F 343 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: F 509 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8122 (t) REVERT: F 515 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7499 (t0) REVERT: F 675 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: F 692 GLU cc_start: 0.6817 (tt0) cc_final: 0.6435 (mm-30) REVERT: F 747 LYS cc_start: 0.3433 (mttt) cc_final: 0.3090 (tmtt) REVERT: F 789 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6166 (p) outliers start: 248 outliers final: 201 residues processed: 399 average time/residue: 0.1360 time to fit residues: 92.7050 Evaluate side-chains 403 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 173 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 LYS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain B residue 806 ASN Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 731 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 791 TYR Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 469 HIS Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 572 PHE Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 739 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 791 TYR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 732 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 789 VAL Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 HIS C 412 ASN ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C 760 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN F 760 ASN ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.088541 restraints weight = 143220.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.088915 restraints weight = 128223.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088842 restraints weight = 108785.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.089152 restraints weight = 102209.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.089146 restraints weight = 90043.213| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 28440 Z= 0.328 Angle : 1.170 11.438 38808 Z= 0.561 Chirality : 0.057 0.249 4710 Planarity : 0.005 0.058 5214 Dihedral : 9.028 50.301 4331 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 18.40 % Favored : 81.56 % Rotamer: Outliers : 9.99 % Allowed : 28.87 % Favored : 61.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.13), residues: 2820 helix: -2.90 (0.30), residues: 204 sheet: -2.38 (0.19), residues: 654 loop : -3.86 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 541 TYR 0.032 0.003 TYR A 579 PHE 0.030 0.003 PHE B 635 TRP 0.011 0.002 TRP D 577 HIS 0.005 0.002 HIS E 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.33 (28434) covalent geometry : angle 1.16933 / 0.56 (38796) SS BOND : bond 0.02890 / 1.58 ( 6) SS BOND : angle 2.85413 / 1.44 ( 12) hydrogen bonds : bond 0.04840 / 2.65 ( 264) hydrogen bonds : angle 7.42718 / 3.74 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 176 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: A 355 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 515 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7098 (t0) REVERT: A 586 LYS cc_start: 0.8813 (mttp) cc_final: 0.8511 (mtmm) REVERT: A 675 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.3670 (m-80) REVERT: A 676 LYS cc_start: 0.6235 (mttt) cc_final: 0.5543 (mttm) REVERT: A 687 LEU cc_start: 0.5020 (OUTLIER) cc_final: 0.4486 (mm) REVERT: A 692 GLU cc_start: 0.7588 (tt0) cc_final: 0.6484 (mm-30) REVERT: A 789 VAL cc_start: 0.6237 (OUTLIER) cc_final: 0.5631 (p) REVERT: B 520 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6926 (tttm) REVERT: B 572 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6390 (t80) REVERT: B 663 MET cc_start: 0.7329 (mmt) cc_final: 0.6707 (mmt) REVERT: B 791 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.4099 (t80) REVERT: C 343 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: C 509 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (t) REVERT: C 515 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7521 (t0) REVERT: C 675 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5706 (m-80) REVERT: C 747 LYS cc_start: 0.3418 (mttt) cc_final: 0.3079 (tmtt) REVERT: D 343 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: D 355 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7874 (p) REVERT: D 515 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7237 (t0) REVERT: D 586 LYS cc_start: 0.8792 (mttp) cc_final: 0.8497 (mtmm) REVERT: D 675 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.3607 (m-80) REVERT: D 676 LYS cc_start: 0.6171 (mttt) cc_final: 0.5502 (mttm) REVERT: D 687 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4502 (mm) REVERT: D 692 GLU cc_start: 0.7565 (tt0) cc_final: 0.6448 (mm-30) REVERT: D 789 VAL cc_start: 0.6180 (OUTLIER) cc_final: 0.5572 (p) REVERT: E 520 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6900 (tttm) REVERT: E 594 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7145 (t80) REVERT: E 663 MET cc_start: 0.7315 (mmt) cc_final: 0.6647 (mmt) REVERT: E 692 GLU cc_start: 0.7469 (tt0) cc_final: 0.6793 (pp20) REVERT: E 791 TYR cc_start: 0.4582 (OUTLIER) cc_final: 0.4086 (t80) REVERT: F 343 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: F 509 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8144 (t) REVERT: F 515 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7539 (t0) REVERT: F 675 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5656 (m-80) REVERT: F 692 GLU cc_start: 0.6803 (tt0) cc_final: 0.6406 (mm-30) REVERT: F 747 LYS cc_start: 0.3426 (mttt) cc_final: 0.3085 (tmtt) REVERT: F 789 VAL cc_start: 0.6477 (OUTLIER) cc_final: 0.6155 (p) outliers start: 235 outliers final: 201 residues processed: 390 average time/residue: 0.1411 time to fit residues: 93.9495 Evaluate side-chains 401 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 173 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 TYR Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 520 LYS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 791 TYR Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 412 ASN Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 626 PHE Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 675 TYR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 711 ASN Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 746 ILE Chi-restraints excluded: chain C residue 760 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 456 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 668 ILE Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 675 TYR Chi-restraints excluded: chain D residue 679 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 ILE Chi-restraints excluded: chain D residue 789 VAL Chi-restraints excluded: chain D residue 791 TYR Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 382 ASN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 469 HIS Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain E residue 520 LYS Chi-restraints excluded: chain E residue 521 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 545 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 568 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 594 PHE Chi-restraints excluded: chain E residue 600 GLU Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain E residue 636 ILE Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 668 ILE Chi-restraints excluded: chain E residue 695 LEU Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 739 VAL Chi-restraints excluded: chain E residue 740 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 751 MET Chi-restraints excluded: chain E residue 791 TYR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain F residue 343 GLN Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 382 ASN Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 463 ASN Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 545 VAL Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 563 SER Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 568 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 622 ASP Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 668 ILE Chi-restraints excluded: chain F residue 669 ASP Chi-restraints excluded: chain F residue 670 SER Chi-restraints excluded: chain F residue 675 TYR Chi-restraints excluded: chain F residue 679 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 695 LEU Chi-restraints excluded: chain F residue 708 THR Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 731 ASN Chi-restraints excluded: chain F residue 740 VAL Chi-restraints excluded: chain F residue 746 ILE Chi-restraints excluded: chain F residue 760 ASN Chi-restraints excluded: chain F residue 789 VAL Chi-restraints excluded: chain F residue 805 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 775 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 = 0.4110 r_free = 0.4110 target = 0.098177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.088501 restraints weight = 143662.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.088861 restraints weight = 129965.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.088757 restraints weight = 110772.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.089003 restraints weight = 106094.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.089069 restraints weight = 93904.995| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.227 28440 Z= 0.358 Angle : 1.286 59.200 38808 Z= 0.652 Chirality : 0.058 0.322 4710 Planarity : 0.006 0.123 5214 Dihedral : 9.025 50.164 4331 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.72 % Favored : 81.21 % Rotamer: Outliers : 10.20 % Allowed : 28.83 % Favored : 60.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.69 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.13), residues: 2820 helix: -2.91 (0.30), residues: 204 sheet: -2.59 (0.19), residues: 684 loop : -3.91 (0.11), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 541 TYR 0.031 0.003 TYR A 579 PHE 0.030 0.003 PHE B 635 TRP 0.023 0.003 TRP D 577 HIS 0.005 0.002 HIS E 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.36 (28434) covalent geometry : angle 1.28520 / 0.65 (38796) SS BOND : bond 0.02895 / 1.58 ( 6) SS BOND : angle 2.86733 / 1.45 ( 12) hydrogen bonds : bond 0.04860 / 2.66 ( 264) hydrogen bonds : angle 7.42311 / 3.74 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6066.66 seconds wall clock time: 105 minutes 24.38 seconds (6324.38 seconds total)