Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 01:53:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_20024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_20024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_20024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_20024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ody_20024/08_2023/6ody_20024.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Residue "A TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/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: 14.23, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 12.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.45 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: 12.07 Time building geometry restraints manager: 13.12 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: 83.41 - 97.12: 10 97.12 - 110.82: 9099 110.82 - 124.53: 28991 124.53 - 138.23: 685 138.23 - 151.94: 11 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 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: 3.310 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: 0.010 Extract box with map and model: 10.440 Check model and map are aligned: 0.410 Set scattering table: 0.290 Process input model: 74.100 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 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 28434 Z= 0.643 Angle : 1.591 37.341 38796 Z= 0.871 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 : 18.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.63 % Favored : 83.33 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.87 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 74 poor density : 274 time to evaluate : 2.756 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 outliers start: 74 outliers final: 32 residues processed: 334 average time/residue: 0.4406 time to fit residues: 223.6684 Evaluate side-chains 206 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 2.809 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2426 time to fit residues: 18.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 601 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN C 625 GLN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** D 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 HIS ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 ASN ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN ** E 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 ASN F 625 GLN ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.193 28434 Z= 1.897 Angle : 2.967 32.503 38796 Z= 1.444 Chirality : 0.135 0.735 4710 Planarity : 0.015 0.135 5214 Dihedral : 14.806 54.331 4302 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 86.69 Ramachandran Plot: Outliers : 1.74 % Allowed : 25.71 % Favored : 72.55 % Rotamer Outliers : 18.15 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 23.33 % Twisted General : 5.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.20 (0.12), residues: 2820 helix: -4.65 (0.18), residues: 138 sheet: -3.37 (0.17), residues: 828 loop : -4.75 (0.10), residues: 1854 *********************** 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 563 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 427 poor density : 136 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 427 outliers final: 276 residues processed: 532 average time/residue: 0.3387 time to fit residues: 299.7743 Evaluate side-chains 412 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 136 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 276 outliers final: 0 residues processed: 276 average time/residue: 0.2606 time to fit residues: 138.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 GLN ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 ASN ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 GLN ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 ASN ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 639 GLN ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.193 28434 Z= 1.898 Angle : 2.990 29.129 38796 Z= 1.458 Chirality : 0.136 0.664 4710 Planarity : 0.016 0.162 5214 Dihedral : 15.531 51.993 4302 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 96.02 Ramachandran Plot: Outliers : 1.31 % Allowed : 31.95 % Favored : 66.74 % Rotamer Outliers : 22.53 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 23.33 % Twisted General : 7.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.66 (0.11), residues: 2820 helix: -5.00 (0.11), residues: 138 sheet: -3.66 (0.17), residues: 786 loop : -5.08 (0.09), residues: 1896 *********************** 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 667 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 530 poor density : 137 time to evaluate : 2.959 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 outliers start: 530 outliers final: 342 residues processed: 624 average time/residue: 0.3553 time to fit residues: 364.6236 Evaluate side-chains 491 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 149 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 342 outliers final: 6 residues processed: 342 average time/residue: 0.2574 time to fit residues: 165.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 733 ASN ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 601 ASN ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.181 28434 Z= 1.895 Angle : 2.983 31.035 38796 Z= 1.454 Chirality : 0.137 0.632 4710 Planarity : 0.016 0.174 5214 Dihedral : 15.843 50.870 4302 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 98.78 Ramachandran Plot: Outliers : 1.45 % Allowed : 34.36 % Favored : 64.18 % Rotamer Outliers : 21.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 23.33 % Twisted General : 7.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.87 (0.10), residues: 2820 helix: -5.16 (0.09), residues: 162 sheet: -3.86 (0.17), residues: 684 loop : -5.18 (0.08), residues: 1974 *********************** 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 649 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 512 poor density : 137 time to evaluate : 2.902 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 outliers start: 512 outliers final: 360 residues processed: 623 average time/residue: 0.3382 time to fit residues: 353.0655 Evaluate side-chains 491 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 131 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 360 outliers final: 6 residues processed: 360 average time/residue: 0.2568 time to fit residues: 175.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.029 0.179 28434 Z= 1.891 Angle : 2.982 26.928 38796 Z= 1.454 Chirality : 0.138 0.617 4710 Planarity : 0.016 0.176 5214 Dihedral : 15.976 56.225 4302 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 99.50 Ramachandran Plot: Outliers : 1.28 % Allowed : 35.92 % Favored : 62.80 % Rotamer Outliers : 19.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 23.33 % Twisted General : 8.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.99 (0.11), residues: 2820 helix: -5.07 (0.11), residues: 138 sheet: -3.84 (0.17), residues: 786 loop : -5.36 (0.08), residues: 1896 *********************** 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 592 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 453 poor density : 139 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 453 outliers final: 296 residues processed: 568 average time/residue: 0.3593 time to fit residues: 334.5246 Evaluate side-chains 436 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 140 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 296 outliers final: 6 residues processed: 296 average time/residue: 0.2610 time to fit residues: 146.6944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 601 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.179 28434 Z= 1.899 Angle : 2.985 30.932 38796 Z= 1.456 Chirality : 0.139 0.615 4710 Planarity : 0.016 0.180 5214 Dihedral : 16.070 57.090 4302 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 100.56 Ramachandran Plot: Outliers : 1.42 % Allowed : 36.21 % Favored : 62.38 % Rotamer Outliers : 17.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 26.67 % Twisted General : 8.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.07 (0.10), residues: 2820 helix: -5.08 (0.11), residues: 138 sheet: -3.84 (0.18), residues: 708 loop : -5.43 (0.07), residues: 1974 *********************** 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 550 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 136 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 414 outliers final: 286 residues processed: 522 average time/residue: 0.3960 time to fit residues: 334.7714 Evaluate side-chains 424 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 138 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 286 outliers final: 6 residues processed: 286 average time/residue: 0.2893 time to fit residues: 156.0962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 601 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.184 28434 Z= 1.910 Angle : 2.991 28.545 38796 Z= 1.461 Chirality : 0.140 0.608 4710 Planarity : 0.016 0.180 5214 Dihedral : 16.152 57.366 4302 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 102.08 Ramachandran Plot: Outliers : 1.38 % Allowed : 36.49 % Favored : 62.13 % Rotamer Outliers : 13.90 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 30.00 % Twisted General : 8.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.28 (0.10), residues: 2820 helix: -5.12 (0.10), residues: 162 sheet: -4.04 (0.16), residues: 786 loop : -5.57 (0.07), residues: 1872 *********************** 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 457 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 130 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 228 residues processed: 435 average time/residue: 0.3780 time to fit residues: 265.3585 Evaluate side-chains 361 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 133 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 228 outliers final: 6 residues processed: 228 average time/residue: 0.2696 time to fit residues: 115.5654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.188 28434 Z= 1.911 Angle : 2.997 24.946 38796 Z= 1.466 Chirality : 0.140 0.656 4710 Planarity : 0.016 0.189 5214 Dihedral : 16.229 56.396 4302 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 103.34 Ramachandran Plot: Outliers : 1.28 % Allowed : 37.27 % Favored : 61.45 % Rotamer Outliers : 8.97 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 30.00 % Twisted General : 8.93 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.30 (0.10), residues: 2820 helix: -5.02 (0.12), residues: 138 sheet: -4.10 (0.16), residues: 786 loop : -5.59 (0.07), residues: 1896 *********************** 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 340 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 129 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 143 residues processed: 321 average time/residue: 0.3840 time to fit residues: 198.8820 Evaluate side-chains 268 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 125 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 143 outliers final: 6 residues processed: 143 average time/residue: 0.2661 time to fit residues: 73.0685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 9.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.189 28434 Z= 1.914 Angle : 3.006 24.895 38796 Z= 1.471 Chirality : 0.140 0.740 4710 Planarity : 0.016 0.179 5214 Dihedral : 16.312 56.509 4302 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 103.34 Ramachandran Plot: Outliers : 1.31 % Allowed : 37.38 % Favored : 61.31 % Rotamer Outliers : 6.76 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 31.67 % Twisted General : 9.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.30 (0.10), residues: 2820 helix: -5.01 (0.12), residues: 138 sheet: -4.26 (0.16), residues: 714 loop : -5.50 (0.07), residues: 1968 *********************** 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 286 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 127 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 101 residues processed: 275 average time/residue: 0.3932 time to fit residues: 174.3250 Evaluate side-chains 226 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 125 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 6 residues processed: 101 average time/residue: 0.2518 time to fit residues: 51.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.186 28434 Z= 1.918 Angle : 3.015 24.830 38796 Z= 1.475 Chirality : 0.139 0.761 4710 Planarity : 0.016 0.179 5214 Dihedral : 16.310 56.724 4302 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 103.26 Ramachandran Plot: Outliers : 1.38 % Allowed : 38.16 % Favored : 60.46 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 30.00 % Twisted General : 9.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.31 (0.10), residues: 2820 helix: -4.93 (0.13), residues: 138 sheet: -4.28 (0.16), residues: 714 loop : -5.50 (0.07), residues: 1968 ********************** 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 210 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 127 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 55 residues processed: 198 average time/residue: 0.4152 time to fit residues: 131.0566 Evaluate side-chains 179 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 2.746 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 6 residues processed: 55 average time/residue: 0.2591 time to fit residues: 29.6853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 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 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 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 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.108007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.096084 restraints weight = 148162.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096271 restraints weight = 112940.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096423 restraints weight = 93268.527| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.030 0.187 28434 Z= 1.920 Angle : 3.016 24.832 38796 Z= 1.475 Chirality : 0.140 0.642 4710 Planarity : 0.016 0.179 5214 Dihedral : 16.334 56.876 4302 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 102.95 Ramachandran Plot: Outliers : 1.35 % Allowed : 37.66 % Favored : 60.99 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 33.33 % Twisted General : 9.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.26 (0.10), residues: 2820 helix: -4.95 (0.14), residues: 126 sheet: -4.34 (0.16), residues: 714 loop : -5.43 (0.08), residues: 1980 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10898.34 seconds wall clock time: 195 minutes 37.12 seconds (11737.12 seconds total)