Starting phenix.real_space_refine (version: dev) on Fri Apr 8 03:07:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/04_2022/6cue_7621_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.015 sd= 0.141 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "c PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 62": "NH1" <-> "NH2" Residue "8 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "q ARG 62": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 31692 Number of models: 1 Model: "" Number of chains: 27 Chain: "c" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "3" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "4" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 104, 'PCIS': 2} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "7" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 97, 'PCIS': 1} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 104, 'PCIS': 2} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 97, 'PCIS': 1} Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "h" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "l" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 104, 'PCIS': 2} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 97, 'PCIS': 1} Chain: "c" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 499 Unusual residues: {'BMA': 6, 'NAG': 27, 'MAN': 5} Classifications: {'undetermined': 38} Link IDs: {None: 37} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 38 Chain: "2" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 499 Unusual residues: {'BMA': 6, 'NAG': 27, 'MAN': 5} Classifications: {'undetermined': 38} Link IDs: {None: 37} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 38 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 499 Unusual residues: {'BMA': 6, 'NAG': 27, 'MAN': 5} Classifications: {'undetermined': 38} Link IDs: {None: 37} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 38 Time building chain proxies: 17.47, per 1000 atoms: 0.55 Number of scatterers: 31692 At special positions: 0 Unit cell: (154, 162.8, 156.2, 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 174 16.00 O 6282 8.00 N 5289 7.00 C 19947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.02 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.02 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 605 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 501 " - pdb=" SG CYS 1 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=1.91 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 93 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 103 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 109 " - pdb=" SG CYS 7 112 " distance=2.00 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=1.94 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.00 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.00 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS q 109 " - pdb=" SG CYS q 112 " distance=1.98 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 88 " distance=2.04 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 Links applied ALPHA1-2 " MAN 2 631 " - " MAN 2 632 " " MAN C 631 " - " MAN C 632 " " MAN c 631 " - " MAN c 632 " ALPHA1-3 " BMA 2 616 " - " MAN 2 617 " " BMA 2 630 " - " MAN 2 631 " " BMA 2 637 " - " MAN 2 638 " " BMA C 616 " - " MAN C 617 " " BMA C 630 " - " MAN C 631 " " BMA C 637 " - " MAN C 638 " " BMA c 616 " - " MAN c 617 " " BMA c 630 " - " MAN c 631 " " BMA c 637 " - " MAN c 638 " ALPHA1-6 " BMA 2 616 " - " MAN 2 618 " " BMA C 616 " - " MAN C 618 " " BMA c 616 " - " MAN c 618 " BETA1-4 " NAG 2 601 " - " NAG 2 602 " " NAG 2 603 " - " NAG 2 604 " " NAG 2 604 " - " BMA 2 605 " " NAG 2 606 " - " NAG 2 607 " " NAG 2 607 " - " BMA 2 608 " " NAG 2 609 " - " NAG 2 610 " " NAG 2 612 " - " NAG 2 613 " " NAG 2 614 " - " NAG 2 615 " " NAG 2 615 " - " BMA 2 616 " " NAG 2 619 " - " NAG 2 620 " " NAG 2 621 " - " NAG 2 622 " " NAG 2 623 " - " NAG 2 624 " " NAG 2 624 " - " BMA 2 625 " " NAG 2 626 " - " NAG 2 627 " " NAG 2 628 " - " NAG 2 629 " " NAG 2 629 " - " BMA 2 630 " " NAG 2 633 " - " NAG 2 634 " " NAG 2 635 " - " NAG 2 636 " " NAG 2 636 " - " BMA 2 637 " " NAG C 601 " - " NAG C 602 " " NAG C 603 " - " NAG C 604 " " NAG C 604 " - " BMA C 605 " " NAG C 606 " - " NAG C 607 " " NAG C 607 " - " BMA C 608 " " NAG C 609 " - " NAG C 610 " " NAG C 612 " - " NAG C 613 " " NAG C 614 " - " NAG C 615 " " NAG C 615 " - " BMA C 616 " " NAG C 619 " - " NAG C 620 " " NAG C 621 " - " NAG C 622 " " NAG C 623 " - " NAG C 624 " " NAG C 624 " - " BMA C 625 " " NAG C 626 " - " NAG C 627 " " NAG C 628 " - " NAG C 629 " " NAG C 629 " - " BMA C 630 " " NAG C 633 " - " NAG C 634 " " NAG C 635 " - " NAG C 636 " " NAG C 636 " - " BMA C 637 " " NAG c 601 " - " NAG c 602 " " NAG c 603 " - " NAG c 604 " " NAG c 604 " - " BMA c 605 " " NAG c 606 " - " NAG c 607 " " NAG c 607 " - " BMA c 608 " " NAG c 609 " - " NAG c 610 " " NAG c 612 " - " NAG c 613 " " NAG c 614 " - " NAG c 615 " " NAG c 615 " - " BMA c 616 " " NAG c 619 " - " NAG c 620 " " NAG c 621 " - " NAG c 622 " " NAG c 623 " - " NAG c 624 " " NAG c 624 " - " BMA c 625 " " NAG c 626 " - " NAG c 627 " " NAG c 628 " - " NAG c 629 " " NAG c 629 " - " BMA c 630 " " NAG c 633 " - " NAG c 634 " " NAG c 635 " - " NAG c 636 " " NAG c 636 " - " BMA c 637 " NAG-ASN " NAG 2 601 " - " ASN 2 133 " " NAG 2 603 " - " ASN 2 137 " " NAG 2 606 " - " ASN 2 156 " " NAG 2 609 " - " ASN 2 160 " " NAG 2 611 " - " ASN 2 197 " " NAG 2 612 " - " ASN 2 234 " " NAG 2 614 " - " ASN 2 262 " " NAG 2 619 " - " ASN 2 295 " " NAG 2 621 " - " ASN 2 301 " " NAG 2 623 " - " ASN 2 363 " " NAG 2 626 " - " ASN 2 386 " " NAG 2 628 " - " ASN 2 332 " " NAG 2 633 " - " ASN 2 448 " " NAG 2 635 " - " ASN 2 276 " " NAG C 601 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 606 " - " ASN C 156 " " NAG C 609 " - " ASN C 160 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 234 " " NAG C 614 " - " ASN C 262 " " NAG C 619 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 623 " - " ASN C 363 " " NAG C 626 " - " ASN C 386 " " NAG C 628 " - " ASN C 332 " " NAG C 633 " - " ASN C 448 " " NAG C 635 " - " ASN C 276 " " NAG c 601 " - " ASN c 133 " " NAG c 603 " - " ASN c 137 " " NAG c 606 " - " ASN c 156 " " NAG c 609 " - " ASN c 160 " " NAG c 611 " - " ASN c 197 " " NAG c 612 " - " ASN c 234 " " NAG c 614 " - " ASN c 262 " " NAG c 619 " - " ASN c 295 " " NAG c 621 " - " ASN c 301 " " NAG c 623 " - " ASN c 363 " " NAG c 626 " - " ASN c 386 " " NAG c 628 " - " ASN c 332 " " NAG c 633 " - " ASN c 448 " " NAG c 635 " - " ASN c 276 " Time building additional restraints: 14.41 Conformation dependent library (CDL) restraints added in 4.7 seconds 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 84 sheets defined 13.7% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'c' and resid 101 through 115 removed outlier: 3.998A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN c 114 " --> pdb=" O SER c 110 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.773A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.500A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.271A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 481 removed outlier: 3.684A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 481 " --> pdb=" O ASP c 477 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.832A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN 2 114 " --> pdb=" O SER 2 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 3.535A pdb=" N LEU 2 125 " --> pdb=" O LEU 2 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 122 through 126' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 Processing helix chain '2' and resid 425 through 429 removed outlier: 4.188A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.671A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.728A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.576A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.558A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.728A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.002A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.810A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 528 removed outlier: 4.017A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 543 removed outlier: 3.807A pdb=" N ALA 1 533 " --> pdb=" O THR 1 529 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET 1 535 " --> pdb=" O GLY 1 531 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU 1 537 " --> pdb=" O ALA 1 533 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR 1 538 " --> pdb=" O SER 1 534 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL 1 539 " --> pdb=" O MET 1 535 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN 1 540 " --> pdb=" O THR 1 536 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 removed outlier: 3.704A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 1 589 " --> pdb=" O ARG 1 585 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 616 removed outlier: 4.335A pdb=" N SER 1 615 " --> pdb=" O ASN 1 611 " (cutoff:3.500A) Processing helix chain '1' and resid 619 through 623 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.914A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 640 through 664 removed outlier: 3.702A pdb=" N GLU 1 647 " --> pdb=" O TYR 1 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 1 648 " --> pdb=" O GLY 1 644 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 1 650 " --> pdb=" O LEU 1 646 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 91 removed outlier: 3.511A pdb=" N SER 3 91 " --> pdb=" O SER 3 88 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 88 removed outlier: 3.540A pdb=" N ASP 4 87 " --> pdb=" O GLU 4 84 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.731A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 100D through 100H removed outlier: 3.526A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '7' and resid 62 through 65 Processing helix chain '7' and resid 94 through 98 removed outlier: 3.760A pdb=" N THR 7 98 " --> pdb=" O PRO 7 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.095A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.629A pdb=" N ALA D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.048A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.299A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.767A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.623A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.569A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.891A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.674A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.752A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 3.842A pdb=" N ALA d 533 " --> pdb=" O THR d 529 " (cutoff:3.500A) Processing helix chain 'd' and resid 536 through 544 removed outlier: 4.081A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS d 574 " --> pdb=" O VAL d 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP d 589 " --> pdb=" O ARG d 585 " (cutoff:3.500A) Processing helix chain 'd' and resid 611 through 616 removed outlier: 4.264A pdb=" N SER d 615 " --> pdb=" O ASN d 611 " (cutoff:3.500A) Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.949A pdb=" N LYS d 633 " --> pdb=" O LEU d 629 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU d 634 " --> pdb=" O GLN d 630 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 640 through 663 removed outlier: 3.617A pdb=" N LYS d 655 " --> pdb=" O ASN d 651 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 84 through 88 removed outlier: 3.556A pdb=" N LEU l 88 " --> pdb=" O ALA l 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.680A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 65 Processing helix chain 'q' and resid 94 through 98 removed outlier: 3.685A pdb=" N THR q 98 " --> pdb=" O PRO q 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.949A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.854A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS c 239 " --> pdb=" O GLU c 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY c 237 " --> pdb=" O PHE c 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.516A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS c 374 " --> pdb=" O CYS c 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.197A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'c' and resid 359 through 360 Processing sheet with id=AB1, first strand: chain 'c' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain '2' and resid 495 through 499 removed outlier: 4.628A pdb=" N VAL 2 36 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR 1 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS 1 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 45 through 47 removed outlier: 4.009A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 75 through 76 removed outlier: 3.952A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 91 through 94 removed outlier: 3.555A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE 2 93 " --> pdb=" O GLY 2 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY 2 237 " --> pdb=" O PHE 2 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain '2' and resid 202 through 203 removed outlier: 6.624A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 260 through 261 removed outlier: 7.138A pdb=" N LEU 2 260 " --> pdb=" O THR 2 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 271 through 273 removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain '2' and resid 359 through 361 removed outlier: 3.510A pdb=" N PHE 2 361 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.837A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.557A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.200A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD3, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.550A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 3 through 5 removed outlier: 4.005A pdb=" N THR 3 78 " --> pdb=" O ASP 3 73 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP 3 73 " --> pdb=" O THR 3 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR 3 71 " --> pdb=" O TYR 3 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 10 through 12 removed outlier: 7.301A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE 3 48 " --> pdb=" O TRP 3 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3' and resid 10 through 12 removed outlier: 3.959A pdb=" N ARG 3 98 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL 3 107 " --> pdb=" O ARG 3 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '4' and resid 5 through 7 removed outlier: 3.508A pdb=" N ASP 4 75 " --> pdb=" O SER 4 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 10 through 12 removed outlier: 6.607A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR 4 92 " --> pdb=" O TYR 4 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '5' and resid 5 through 7 Processing sheet with id=AE1, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AE2, first strand: chain '5' and resid 46 through 51 removed outlier: 6.401A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AE4, first strand: chain '6' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain '6' and resid 44 through 48 removed outlier: 6.588A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 3 through 5 Processing sheet with id=AE7, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG 7 38 " --> pdb=" O TRP 7 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP 7 47 " --> pdb=" O ARG 7 38 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE 7 40 " --> pdb=" O PHE 7 45 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE 7 45 " --> pdb=" O ILE 7 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR 7 119 " --> pdb=" O ARG 7 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '8' and resid 4 through 7 removed outlier: 3.591A pdb=" N CYS 8 23 " --> pdb=" O PHE 8 71 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE 8 71 " --> pdb=" O CYS 8 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '8' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain '8' and resid 53 through 54 removed outlier: 5.754A pdb=" N LEU 8 46 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN 8 37 " --> pdb=" O LEU 8 46 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE 8 48 " --> pdb=" O TRP 8 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.360A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 72 through 73 removed outlier: 4.133A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.683A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.696A pdb=" N VAL M 107 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA M 88 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AG4, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.547A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AG7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.693A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Q 40 " --> pdb=" O GLY Q 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 57 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.796A pdb=" N CYS Q 103 " --> pdb=" O TRP Q 120 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP Q 120 " --> pdb=" O CYS Q 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 105 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.741A pdb=" N PHE R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'R' and resid 53 through 54 removed outlier: 5.702A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER h 97 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET h 34 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG h 98 " --> pdb=" O VAL h 107 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL h 107 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'h' and resid 39 through 40 Processing sheet with id=AH7, first strand: chain 'h' and resid 72 through 73 removed outlier: 3.980A pdb=" N ASP h 73 " --> pdb=" O THR h 78 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'l' and resid 5 through 7 removed outlier: 3.620A pdb=" N ASP l 75 " --> pdb=" O SER l 72 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.438A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'l' and resid 40 through 41 removed outlier: 6.575A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AI3, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL m 107 " --> pdb=" O ALA m 88 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA m 88 " --> pdb=" O VAL m 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AI5, first strand: chain 'n' and resid 11 through 13 removed outlier: 3.657A pdb=" N VAL n 11 " --> pdb=" O THR n 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE n 105 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU n 104 " --> pdb=" O ALA n 84 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'n' and resid 18 through 23 Processing sheet with id=AI7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'q' and resid 10 through 12 removed outlier: 5.779A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'q' and resid 10 through 12 removed outlier: 6.958A pdb=" N CYS q 103 " --> pdb=" O TRP q 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP q 120 " --> pdb=" O CYS q 103 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG q 105 " --> pdb=" O GLN q 118 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 4 through 7 removed outlier: 3.591A pdb=" N PHE r 71 " --> pdb=" O CYS r 23 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AJ3, first strand: chain 'r' and resid 53 through 54 removed outlier: 5.688A pdb=" N LEU r 46 " --> pdb=" O GLN r 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN r 37 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE r 48 " --> pdb=" O TRP r 35 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2454 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: 12.54 Time building geometry restraints manager: 15.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9798 1.34 - 1.46: 8565 1.46 - 1.59: 13804 1.59 - 1.71: 2 1.71 - 1.84: 234 Bond restraints: 32403 Sorted by residual: bond pdb=" C LYS C 252 " pdb=" N PRO C 253 " ideal model delta sigma weight residual 1.335 1.304 0.031 8.70e-03 1.32e+04 1.30e+01 bond pdb=" CA TYR L 54 " pdb=" CB TYR L 54 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.20e-02 2.07e+03 1.06e+01 bond pdb=" C TYR C 435 " pdb=" N ALA C 436 " ideal model delta sigma weight residual 1.331 1.273 0.058 2.07e-02 2.33e+03 7.78e+00 bond pdb=" N PHE r 91 " pdb=" CA PHE r 91 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N PHE R 91 " pdb=" CA PHE R 91 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 32398 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.81: 417 103.81 - 111.41: 14382 111.41 - 119.02: 12169 119.02 - 126.62: 16431 126.62 - 134.22: 626 Bond angle restraints: 44025 Sorted by residual: angle pdb=" C TYR r 49 " pdb=" N ASP r 50 " pdb=" CA ASP r 50 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C ASN C 99 " pdb=" N MET C 100 " pdb=" CA MET C 100 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C TYR R 49 " pdb=" N ASP R 50 " pdb=" CA ASP R 50 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C ASN c 99 " pdb=" N MET c 100 " pdb=" CA MET c 100 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C TYR 8 49 " pdb=" N ASP 8 50 " pdb=" CA ASP 8 50 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 ... (remaining 44020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.62: 18392 18.62 - 37.24: 607 37.24 - 55.86: 116 55.86 - 74.47: 12 74.47 - 93.09: 16 Dihedral angle restraints: 19143 sinusoidal: 8115 harmonic: 11028 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual 93.00 175.73 -82.73 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS 2 201 " pdb=" SG CYS 2 201 " pdb=" SG CYS 2 433 " pdb=" CB CYS 2 433 " ideal model delta sinusoidal sigma weight residual 93.00 169.42 -76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA GLN r 90 " pdb=" C GLN r 90 " pdb=" N PHE r 91 " pdb=" CA PHE r 91 " ideal model delta harmonic sigma weight residual 180.00 -139.91 -40.09 0 5.00e+00 4.00e-02 6.43e+01 ... (remaining 19140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 5176 0.244 - 0.488: 17 0.488 - 0.731: 3 0.731 - 0.975: 1 0.975 - 1.219: 2 Chirality restraints: 5199 Sorted by residual: chirality pdb=" C1 NAG 2 623 " pdb=" ND2 ASN 2 363 " pdb=" C2 NAG 2 623 " pdb=" O5 NAG 2 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.71e+01 chirality pdb=" C1 NAG C 623 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG C 623 " pdb=" O5 NAG C 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" C1 NAG c 623 " pdb=" ND2 ASN c 363 " pdb=" C2 NAG c 623 " pdb=" O5 NAG c 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 ... (remaining 5196 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " 0.060 2.00e-02 2.50e+03 8.01e-02 8.03e+01 pdb=" CG ASN C 386 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " -0.138 2.00e-02 2.50e+03 pdb=" C1 NAG C 626 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 386 " -0.043 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN 2 386 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 386 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 386 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG 2 626 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 386 " 0.036 2.00e-02 2.50e+03 5.00e-02 3.13e+01 pdb=" CG ASN c 386 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN c 386 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN c 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG c 626 " 0.058 2.00e-02 2.50e+03 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 869 2.68 - 3.23: 28028 3.23 - 3.79: 48079 3.79 - 4.34: 60139 4.34 - 4.90: 100563 Nonbonded interactions: 237678 Sorted by model distance: nonbonded pdb=" NH2 ARG D 542 " pdb=" OE2 GLU d 647 " model vdw 2.121 2.520 nonbonded pdb=" OD2 ASP c 457 " pdb=" NH1 ARG c 469 " model vdw 2.134 2.520 nonbonded pdb=" NH2 ARG 1 542 " pdb=" OE2 GLU D 647 " model vdw 2.174 2.520 nonbonded pdb=" OE2 GLU 1 647 " pdb=" NH2 ARG d 542 " model vdw 2.177 2.520 nonbonded pdb=" N THR M 83 " pdb=" OD2 ASP M 86 " model vdw 2.180 2.520 ... (remaining 237673 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 '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '8' selection = chain 'R' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 19947 2.51 5 N 5289 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.720 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: 0.030 Extract box with map and model: 14.000 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.270 Process input model: 82.650 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.007 0.083 32403 Z= 0.483 Angle : 0.952 11.437 44025 Z= 0.526 Chirality : 0.066 1.219 5199 Planarity : 0.007 0.070 5448 Dihedral : 9.981 93.092 11916 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.55 (0.12), residues: 3783 helix: -3.21 (0.17), residues: 366 sheet: -1.85 (0.14), residues: 1236 loop : -2.57 (0.11), residues: 2181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 647 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 654 average time/residue: 0.4789 time to fit residues: 475.5566 Evaluate side-chains 276 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 273 time to evaluate : 3.576 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2504 time to fit residues: 6.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 10.0000 chunk 284 optimal weight: 0.2980 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN c 315 GLN c 356 ASN 2 33 ASN 2 356 ASN C 33 ASN C 85 HIS 1 625 ASN 4 27 GLN 4 58 ASN 5 1 GLN 5 3 HIS 5 52 HIS 7 3 GLN 7 118 GLN L 27 GLN L 58 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 118 GLN l 58 ASN ** l 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN q 6 GLN q 118 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 32403 Z= 0.296 Angle : 0.734 13.135 44025 Z= 0.378 Chirality : 0.047 0.295 5199 Planarity : 0.005 0.052 5448 Dihedral : 7.353 92.939 4980 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.13), residues: 3783 helix: -1.39 (0.23), residues: 405 sheet: -1.71 (0.14), residues: 1308 loop : -2.05 (0.12), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 335 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 39 residues processed: 386 average time/residue: 0.4469 time to fit residues: 283.7025 Evaluate side-chains 312 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3158 time to fit residues: 27.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 chunk 368 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN C 183 GLN ** 1 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 5 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 GLN 8 89 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN l 95 GLN q 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 32403 Z= 0.209 Angle : 0.661 13.367 44025 Z= 0.338 Chirality : 0.045 0.299 5199 Planarity : 0.004 0.068 5448 Dihedral : 6.933 95.216 4980 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 3783 helix: -0.48 (0.26), residues: 387 sheet: -1.41 (0.14), residues: 1401 loop : -1.84 (0.13), residues: 1995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 21 residues processed: 371 average time/residue: 0.4208 time to fit residues: 253.6178 Evaluate side-chains 285 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 264 time to evaluate : 4.189 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3427 time to fit residues: 17.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN c 315 GLN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 432 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 44 GLN 6 89 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 1 GLN d 575 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.109 32403 Z= 0.613 Angle : 0.882 17.389 44025 Z= 0.446 Chirality : 0.050 0.327 5199 Planarity : 0.006 0.091 5448 Dihedral : 7.340 91.466 4980 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.33 (0.13), residues: 3783 helix: -0.36 (0.25), residues: 414 sheet: -1.26 (0.15), residues: 1314 loop : -2.01 (0.13), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 254 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 65 residues processed: 337 average time/residue: 0.4049 time to fit residues: 226.6683 Evaluate side-chains 301 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 3.978 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.2946 time to fit residues: 41.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.4980 chunk 205 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 309 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 374 HIS C 72 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 32403 Z= 0.192 Angle : 0.660 13.373 44025 Z= 0.335 Chirality : 0.046 0.306 5199 Planarity : 0.004 0.048 5448 Dihedral : 6.748 95.354 4980 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3783 helix: 0.06 (0.26), residues: 414 sheet: -1.20 (0.14), residues: 1353 loop : -1.69 (0.13), residues: 2016 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 292 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 334 average time/residue: 0.4008 time to fit residues: 222.0104 Evaluate side-chains 271 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 4.042 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.2779 time to fit residues: 17.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.7980 chunk 326 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 301 optimal weight: 0.3980 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 32403 Z= 0.227 Angle : 0.635 11.477 44025 Z= 0.323 Chirality : 0.045 0.302 5199 Planarity : 0.004 0.085 5448 Dihedral : 6.562 94.459 4980 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3783 helix: 0.50 (0.27), residues: 396 sheet: -1.13 (0.14), residues: 1332 loop : -1.61 (0.13), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 314 average time/residue: 0.4100 time to fit residues: 213.3284 Evaluate side-chains 281 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 3.690 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.2673 time to fit residues: 18.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 89 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 575 GLN ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 32403 Z= 0.300 Angle : 0.666 14.377 44025 Z= 0.336 Chirality : 0.045 0.302 5199 Planarity : 0.004 0.063 5448 Dihedral : 6.576 93.815 4980 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3783 helix: 0.58 (0.27), residues: 396 sheet: -1.08 (0.14), residues: 1332 loop : -1.56 (0.14), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 290 average time/residue: 0.4102 time to fit residues: 197.0748 Evaluate side-chains 260 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 3.682 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.2844 time to fit residues: 17.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 425 ASN ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN 5 1 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 32403 Z= 0.187 Angle : 0.626 12.917 44025 Z= 0.315 Chirality : 0.044 0.301 5199 Planarity : 0.004 0.055 5448 Dihedral : 6.398 94.892 4980 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3783 helix: 0.52 (0.27), residues: 417 sheet: -0.85 (0.14), residues: 1320 loop : -1.47 (0.14), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 275 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 292 average time/residue: 0.4218 time to fit residues: 203.8157 Evaluate side-chains 267 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 3.782 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.2939 time to fit residues: 16.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 3.9990 chunk 346 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 202 optimal weight: 0.0010 chunk 146 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 335 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 32403 Z= 0.309 Angle : 0.680 13.458 44025 Z= 0.339 Chirality : 0.045 0.300 5199 Planarity : 0.004 0.051 5448 Dihedral : 6.467 93.196 4980 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3783 helix: 0.88 (0.27), residues: 396 sheet: -0.83 (0.14), residues: 1347 loop : -1.54 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 4.081 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: 31 outliers final: 19 residues processed: 270 average time/residue: 0.4155 time to fit residues: 188.4384 Evaluate side-chains 252 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 3.667 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.2826 time to fit residues: 14.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.0970 chunk 356 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 247 optimal weight: 30.0000 chunk 373 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 297 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 229 optimal weight: 0.1980 chunk 182 optimal weight: 10.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 1 GLN m 3 HIS ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.170 32403 Z= 0.195 Angle : 0.666 15.511 44025 Z= 0.333 Chirality : 0.045 0.299 5199 Planarity : 0.005 0.160 5448 Dihedral : 6.346 95.131 4980 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3783 helix: 0.74 (0.27), residues: 417 sheet: -0.82 (0.14), residues: 1350 loop : -1.39 (0.14), residues: 2016 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 270 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 278 average time/residue: 0.4100 time to fit residues: 189.5629 Evaluate side-chains 252 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 3.903 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2922 time to fit residues: 7.8120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 274 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.078392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055515 restraints weight = 138440.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.056626 restraints weight = 82621.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.056570 restraints weight = 58755.283| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.130 32403 Z= 0.191 Angle : 0.651 13.151 44025 Z= 0.324 Chirality : 0.044 0.294 5199 Planarity : 0.004 0.129 5448 Dihedral : 6.247 95.176 4980 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3783 helix: 0.79 (0.27), residues: 417 sheet: -0.61 (0.14), residues: 1347 loop : -1.42 (0.14), residues: 2019 =============================================================================== Job complete usr+sys time: 5454.70 seconds wall clock time: 101 minutes 46.61 seconds (6106.61 seconds total)