Starting phenix.real_space_refine on Thu Feb 15 19:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/02_2024/7kew_22841.pdb" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8325 2.51 5 N 2235 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 545": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13173 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "B" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.16, per 1000 atoms: 0.54 Number of scatterers: 13173 At special positions: 0 Unit cell: (136.99, 151.41, 129.78, 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 63 16.00 O 2550 8.00 N 2235 7.00 C 8325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS D 609 " distance=2.08 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.10 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS E 609 " distance=2.08 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.10 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.08 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.10 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " 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 ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG B 401 " - " ASN B 228 " " NAG C 401 " - " ASN C 228 " " NAG M 1 " - " ASN B 257 " " NAG N 1 " - " ASN A 257 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.1% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'E' and resid 553 through 575 removed outlier: 3.511A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'F' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing sheet with id=AA1, first strand: chain 'D' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 136 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 138 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 274 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER G 59 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 35 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE G 100E" --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU G 96 " --> pdb=" O PHE G 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 94 " --> pdb=" O SER G 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA6, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 601 through 602 removed outlier: 6.879A pdb=" N CYS D 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'E' and resid 543 through 549 removed outlier: 5.538A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 136 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 138 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 274 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER H 59 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE H 35 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE H 100E" --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU H 96 " --> pdb=" O PHE H 100E" (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 94 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AC4, first strand: chain 'F' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG C 136 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 138 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 274 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER I 59 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 35 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 100E through 103 removed outlier: 6.928A pdb=" N PHE I 100E" --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU I 96 " --> pdb=" O PHE I 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG I 94 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1302 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: 4.24 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2227 1.31 - 1.45: 4355 1.45 - 1.59: 6747 1.59 - 1.73: 66 1.73 - 1.87: 78 Bond restraints: 13473 Sorted by residual: bond pdb=" CB ILE C 33 " pdb=" CG1 ILE C 33 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" NE1 TRP I 103 " pdb=" CE2 TRP I 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.34e+01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" NE1 TRP G 103 " pdb=" CE2 TRP G 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.23e+01 ... (remaining 13468 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.11: 801 107.11 - 113.85: 6903 113.85 - 120.59: 5738 120.59 - 127.33: 4682 127.33 - 134.07: 176 Bond angle restraints: 18300 Sorted by residual: angle pdb=" N GLU C 71 " pdb=" CA GLU C 71 " pdb=" C GLU C 71 " ideal model delta sigma weight residual 114.62 104.18 10.44 1.14e+00 7.69e-01 8.39e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 114.62 104.26 10.36 1.14e+00 7.69e-01 8.26e+01 angle pdb=" N GLU A 71 " pdb=" CA GLU A 71 " pdb=" C GLU A 71 " ideal model delta sigma weight residual 114.62 104.27 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" N ARG C 247 " pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 114.75 104.25 10.50 1.26e+00 6.30e-01 6.95e+01 angle pdb=" N ARG A 247 " pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.86e+01 ... (remaining 18295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 8046 21.41 - 42.81: 156 42.81 - 64.22: 45 64.22 - 85.63: 27 85.63 - 107.03: 12 Dihedral angle restraints: 8286 sinusoidal: 3579 harmonic: 4707 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.17 40.83 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.18 40.82 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 8283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1453 0.103 - 0.207: 482 0.207 - 0.310: 128 0.310 - 0.414: 30 0.414 - 0.517: 13 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 ... (remaining 2103 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 103 " -0.065 2.00e-02 2.50e+03 3.04e-02 2.31e+01 pdb=" CG TRP H 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 103 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 103 " -0.065 2.00e-02 2.50e+03 3.03e-02 2.29e+01 pdb=" CG TRP I 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP I 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 103 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 103 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 103 " -0.065 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CG TRP G 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP G 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 103 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP G 103 " -0.027 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5329 2.90 - 3.40: 12294 3.40 - 3.90: 23301 3.90 - 4.40: 26627 4.40 - 4.90: 41730 Nonbonded interactions: 109281 Sorted by model distance: nonbonded pdb=" N PRO B 187 " pdb=" O PRO B 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO C 187 " pdb=" O PRO C 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO A 187 " pdb=" O PRO A 187 " model vdw 2.403 2.496 nonbonded pdb=" N ARG C 247 " pdb=" N PHE C 248 " model vdw 2.443 2.560 nonbonded pdb=" N ARG B 247 " pdb=" N PHE B 248 " model vdw 2.444 2.560 ... (remaining 109276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.610 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.460 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.022 0.136 13473 Z= 1.407 Angle : 1.882 13.024 18300 Z= 1.237 Chirality : 0.117 0.517 2106 Planarity : 0.009 0.037 2310 Dihedral : 11.742 107.032 5211 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.16 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1614 helix: -0.03 (0.30), residues: 210 sheet: -0.04 (0.25), residues: 438 loop : 0.31 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.013 TRP H 103 HIS 0.008 0.002 HIS C 238 PHE 0.031 0.007 PHE H 29 TYR 0.066 0.013 TYR D 534 ARG 0.007 0.001 ARG F 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.525 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: A 156 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6660 (tp30) REVERT: A 230 THR cc_start: 0.7277 (m) cc_final: 0.6749 (m) REVERT: A 235 GLN cc_start: 0.9171 (tt0) cc_final: 0.8890 (tm-30) REVERT: G 48 MET cc_start: 0.8819 (mtp) cc_final: 0.8369 (mtp) REVERT: J 70 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8777 (mm-30) REVERT: J 97 THR cc_start: 0.7532 (t) cc_final: 0.6244 (p) REVERT: B 156 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6768 (tp30) REVERT: B 235 GLN cc_start: 0.9153 (tt0) cc_final: 0.8672 (tm-30) REVERT: H 48 MET cc_start: 0.8772 (mtp) cc_final: 0.8325 (mtp) REVERT: H 101 ASP cc_start: 0.7210 (m-30) cc_final: 0.6877 (m-30) REVERT: K 70 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8885 (mm-30) REVERT: K 97 THR cc_start: 0.7740 (t) cc_final: 0.6526 (p) REVERT: C 156 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6595 (tp30) REVERT: C 230 THR cc_start: 0.7141 (m) cc_final: 0.6461 (m) REVERT: C 235 GLN cc_start: 0.9246 (tt0) cc_final: 0.8941 (tm-30) REVERT: I 23 ARG cc_start: 0.9050 (ttt180) cc_final: 0.8843 (tpp80) REVERT: I 48 MET cc_start: 0.8804 (mtp) cc_final: 0.8357 (mtp) REVERT: I 68 THR cc_start: 0.8376 (m) cc_final: 0.8108 (p) REVERT: I 81 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7233 (mt-10) REVERT: I 101 ASP cc_start: 0.7397 (m-30) cc_final: 0.6888 (m-30) REVERT: L 70 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8859 (mm-30) REVERT: L 97 THR cc_start: 0.7493 (t) cc_final: 0.6182 (p) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2990 time to fit residues: 207.0276 Evaluate side-chains 228 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN D 602 HIS H 64 GLN K 32 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 602 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN F 602 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13473 Z= 0.296 Angle : 0.799 9.108 18300 Z= 0.425 Chirality : 0.050 0.223 2106 Planarity : 0.005 0.054 2310 Dihedral : 10.359 85.144 2268 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.33 (0.20), residues: 1614 helix: 0.40 (0.34), residues: 231 sheet: 0.10 (0.27), residues: 387 loop : -0.46 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 275 HIS 0.006 0.002 HIS I 100C PHE 0.046 0.003 PHE G 29 TYR 0.034 0.003 TYR D 534 ARG 0.006 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.635 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 REVERT: A 120 GLU cc_start: 0.7692 (mp0) cc_final: 0.7361 (mt-10) REVERT: A 126 PRO cc_start: 0.7999 (Cg_exo) cc_final: 0.7569 (Cg_endo) REVERT: A 235 GLN cc_start: 0.9182 (tt0) cc_final: 0.8856 (tm-30) REVERT: G 23 ARG cc_start: 0.8981 (ttt180) cc_final: 0.8777 (tpt-90) REVERT: G 37 VAL cc_start: 0.8544 (m) cc_final: 0.8337 (m) REVERT: G 46 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7893 (mm-30) REVERT: G 48 MET cc_start: 0.8889 (mtp) cc_final: 0.8488 (mtp) REVERT: G 53 ILE cc_start: 0.8185 (tt) cc_final: 0.7882 (mm) REVERT: J 70 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9001 (mm-30) REVERT: J 97 THR cc_start: 0.6775 (t) cc_final: 0.5674 (p) REVERT: B 120 GLU cc_start: 0.7275 (pp20) cc_final: 0.7040 (pp20) REVERT: B 156 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7061 (tp30) REVERT: B 235 GLN cc_start: 0.9219 (tt0) cc_final: 0.8684 (tm-30) REVERT: H 20 VAL cc_start: 0.8794 (t) cc_final: 0.8505 (p) REVERT: H 46 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7241 (mm-30) REVERT: K 35 TRP cc_start: 0.5683 (m-90) cc_final: 0.5412 (m-90) REVERT: K 48 ILE cc_start: 0.7486 (mm) cc_final: 0.6776 (mm) REVERT: K 97 THR cc_start: 0.7063 (t) cc_final: 0.6774 (p) REVERT: C 156 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6993 (tp30) REVERT: C 235 GLN cc_start: 0.9225 (tt0) cc_final: 0.8910 (tm-30) REVERT: I 20 VAL cc_start: 0.8810 (t) cc_final: 0.8569 (t) REVERT: I 32 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8634 (tptp) REVERT: I 46 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7268 (mm-30) REVERT: I 48 MET cc_start: 0.8914 (mtp) cc_final: 0.8577 (mtp) REVERT: I 90 TYR cc_start: 0.8298 (m-80) cc_final: 0.8028 (m-80) REVERT: I 96 GLU cc_start: 0.7784 (tt0) cc_final: 0.7188 (tp30) REVERT: L 70 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9042 (mm-30) REVERT: L 97 THR cc_start: 0.6822 (t) cc_final: 0.6508 (p) REVERT: L 103 LYS cc_start: 0.8176 (tttt) cc_final: 0.7950 (tttm) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2952 time to fit residues: 136.5621 Evaluate side-chains 228 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN C 69 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13473 Z= 0.283 Angle : 0.750 9.943 18300 Z= 0.393 Chirality : 0.049 0.271 2106 Planarity : 0.005 0.043 2310 Dihedral : 9.446 77.080 2268 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.67 (0.21), residues: 1614 helix: 0.74 (0.36), residues: 234 sheet: -0.53 (0.23), residues: 486 loop : -0.65 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 275 HIS 0.008 0.002 HIS F 602 PHE 0.031 0.002 PHE G 29 TYR 0.029 0.002 TYR D 534 ARG 0.005 0.001 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.529 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: A 229 MET cc_start: 0.8113 (pmm) cc_final: 0.7906 (pmm) REVERT: A 235 GLN cc_start: 0.9138 (tt0) cc_final: 0.8535 (tm-30) REVERT: G 19 LYS cc_start: 0.8961 (tptt) cc_final: 0.8651 (tptp) REVERT: G 23 ARG cc_start: 0.8986 (ttt180) cc_final: 0.8702 (ttm-80) REVERT: G 32 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8888 (tptp) REVERT: G 48 MET cc_start: 0.9056 (mtp) cc_final: 0.8724 (mtp) REVERT: J 33 LEU cc_start: 0.8974 (tp) cc_final: 0.8687 (tp) REVERT: J 71 PHE cc_start: 0.8342 (m-80) cc_final: 0.7086 (m-10) REVERT: J 90 GLN cc_start: 0.8416 (tt0) cc_final: 0.8113 (tt0) REVERT: J 97 THR cc_start: 0.7468 (t) cc_final: 0.7115 (p) REVERT: B 156 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7337 (tp30) REVERT: B 229 MET cc_start: 0.8236 (pmm) cc_final: 0.8004 (pmm) REVERT: B 235 GLN cc_start: 0.9160 (tt0) cc_final: 0.8583 (tm-30) REVERT: H 23 ARG cc_start: 0.8712 (tpt-90) cc_final: 0.8504 (tpp80) REVERT: H 35 SER cc_start: 0.8678 (t) cc_final: 0.8351 (m) REVERT: H 48 MET cc_start: 0.8528 (mtt) cc_final: 0.8069 (mtt) REVERT: H 98 ILE cc_start: 0.5432 (mm) cc_final: 0.5230 (mm) REVERT: K 90 GLN cc_start: 0.7659 (tt0) cc_final: 0.7008 (tt0) REVERT: K 97 THR cc_start: 0.7484 (t) cc_final: 0.6236 (p) REVERT: C 235 GLN cc_start: 0.9256 (tt0) cc_final: 0.8868 (tm-30) REVERT: I 46 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7764 (mm-30) REVERT: I 48 MET cc_start: 0.9120 (mtp) cc_final: 0.8711 (mtp) REVERT: L 70 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9141 (mm-30) REVERT: L 71 PHE cc_start: 0.8162 (m-10) cc_final: 0.7681 (m-10) REVERT: L 90 GLN cc_start: 0.7604 (tt0) cc_final: 0.7142 (tt0) REVERT: L 97 THR cc_start: 0.7158 (t) cc_final: 0.6280 (p) REVERT: F 596 ARG cc_start: 0.7404 (mpt180) cc_final: 0.7151 (mmm160) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2821 time to fit residues: 124.5018 Evaluate side-chains 213 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 30.0000 chunk 153 optimal weight: 0.0030 chunk 137 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS C 263 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13473 Z= 0.385 Angle : 0.824 10.439 18300 Z= 0.427 Chirality : 0.051 0.240 2106 Planarity : 0.006 0.065 2310 Dihedral : 8.881 67.598 2268 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.02 (0.20), residues: 1614 helix: 0.75 (0.35), residues: 216 sheet: -0.61 (0.23), residues: 504 loop : -1.05 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP I 103 HIS 0.007 0.002 HIS H 100C PHE 0.025 0.003 PHE E 592 TYR 0.021 0.003 TYR E 534 ARG 0.005 0.001 ARG H 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.455 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: A 77 THR cc_start: 0.7515 (p) cc_final: 0.6804 (t) REVERT: A 120 GLU cc_start: 0.8664 (mp0) cc_final: 0.8411 (mp0) REVERT: A 122 LEU cc_start: 0.9037 (mm) cc_final: 0.8672 (mm) REVERT: A 167 SER cc_start: 0.8664 (t) cc_final: 0.8144 (p) REVERT: A 229 MET cc_start: 0.8441 (pmm) cc_final: 0.8201 (pmm) REVERT: A 230 THR cc_start: 0.7302 (m) cc_final: 0.7066 (m) REVERT: A 235 GLN cc_start: 0.9157 (tt0) cc_final: 0.8524 (tm-30) REVERT: G 48 MET cc_start: 0.9105 (mtp) cc_final: 0.8825 (mtp) REVERT: G 52 MET cc_start: 0.8735 (mmp) cc_final: 0.8459 (mmm) REVERT: G 81 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7377 (tp30) REVERT: G 90 TYR cc_start: 0.8626 (m-10) cc_final: 0.8282 (m-80) REVERT: J 3 VAL cc_start: 0.5543 (t) cc_final: 0.5297 (t) REVERT: J 33 LEU cc_start: 0.8934 (tp) cc_final: 0.8596 (tp) REVERT: J 71 PHE cc_start: 0.8491 (m-80) cc_final: 0.7532 (m-10) REVERT: J 90 GLN cc_start: 0.7910 (tt0) cc_final: 0.7268 (tt0) REVERT: J 97 THR cc_start: 0.7525 (t) cc_final: 0.6798 (p) REVERT: D 602 HIS cc_start: 0.7130 (t70) cc_final: 0.6318 (m170) REVERT: B 77 THR cc_start: 0.7617 (p) cc_final: 0.7159 (t) REVERT: B 120 GLU cc_start: 0.7724 (pp20) cc_final: 0.7293 (pp20) REVERT: B 229 MET cc_start: 0.8478 (pmm) cc_final: 0.8232 (pmm) REVERT: B 230 THR cc_start: 0.7112 (m) cc_final: 0.6879 (m) REVERT: B 235 GLN cc_start: 0.9158 (tt0) cc_final: 0.8482 (tm-30) REVERT: H 19 LYS cc_start: 0.8660 (tptt) cc_final: 0.8459 (tptp) REVERT: H 20 VAL cc_start: 0.8882 (t) cc_final: 0.8381 (t) REVERT: H 52 MET cc_start: 0.8311 (mmm) cc_final: 0.8073 (mmm) REVERT: H 80 MET cc_start: 0.8306 (mtp) cc_final: 0.8103 (mtp) REVERT: K 27 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7417 (tm-30) REVERT: K 71 PHE cc_start: 0.8640 (m-10) cc_final: 0.7925 (m-10) REVERT: K 90 GLN cc_start: 0.7885 (tt0) cc_final: 0.7253 (tt0) REVERT: K 97 THR cc_start: 0.7697 (t) cc_final: 0.7075 (p) REVERT: E 588 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8836 (mmmm) REVERT: C 77 THR cc_start: 0.7379 (p) cc_final: 0.6771 (t) REVERT: C 229 MET cc_start: 0.8444 (pmm) cc_final: 0.8158 (pmm) REVERT: C 230 THR cc_start: 0.7006 (m) cc_final: 0.6715 (m) REVERT: C 235 GLN cc_start: 0.9248 (tt0) cc_final: 0.8558 (tm-30) REVERT: I 19 LYS cc_start: 0.8959 (tppt) cc_final: 0.8717 (mmmt) REVERT: I 46 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7736 (mm-30) REVERT: I 48 MET cc_start: 0.9282 (mtp) cc_final: 0.9020 (mtp) REVERT: I 52 MET cc_start: 0.8509 (mpp) cc_final: 0.8001 (mpp) REVERT: I 64 GLN cc_start: 0.8392 (mt0) cc_final: 0.8026 (tp40) REVERT: I 96 GLU cc_start: 0.7902 (tt0) cc_final: 0.7646 (tp30) REVERT: L 27 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7568 (tm-30) REVERT: L 70 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9135 (mm-30) REVERT: L 90 GLN cc_start: 0.7868 (tt0) cc_final: 0.7287 (tt0) REVERT: L 97 THR cc_start: 0.7506 (t) cc_final: 0.6801 (p) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2598 time to fit residues: 109.8923 Evaluate side-chains 208 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 263 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 263 ASN L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 13473 Z= 0.504 Angle : 0.925 12.369 18300 Z= 0.474 Chirality : 0.054 0.286 2106 Planarity : 0.007 0.051 2310 Dihedral : 9.047 62.512 2268 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.20), residues: 1614 helix: 0.06 (0.33), residues: 216 sheet: -0.88 (0.22), residues: 504 loop : -1.40 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP K 35 HIS 0.011 0.003 HIS A 154 PHE 0.022 0.003 PHE G 29 TYR 0.044 0.003 TYR E 534 ARG 0.017 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 1.626 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: A 77 THR cc_start: 0.8166 (p) cc_final: 0.7605 (t) REVERT: A 122 LEU cc_start: 0.9232 (mm) cc_final: 0.8763 (mm) REVERT: A 172 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7653 (ptp90) REVERT: A 229 MET cc_start: 0.8644 (pmm) cc_final: 0.8394 (pmm) REVERT: A 230 THR cc_start: 0.7366 (m) cc_final: 0.7033 (m) REVERT: A 235 GLN cc_start: 0.9184 (tt0) cc_final: 0.8595 (tm-30) REVERT: G 64 GLN cc_start: 0.8077 (mm110) cc_final: 0.7848 (mm-40) REVERT: G 90 TYR cc_start: 0.8633 (m-10) cc_final: 0.8115 (m-80) REVERT: G 94 ARG cc_start: 0.7475 (mmt-90) cc_final: 0.7139 (mtp85) REVERT: G 97 ILE cc_start: 0.8319 (pt) cc_final: 0.7650 (mm) REVERT: J 90 GLN cc_start: 0.8557 (tt0) cc_final: 0.8032 (tt0) REVERT: J 97 THR cc_start: 0.7807 (t) cc_final: 0.7327 (p) REVERT: D 602 HIS cc_start: 0.6938 (t70) cc_final: 0.6032 (m170) REVERT: B 77 THR cc_start: 0.8136 (p) cc_final: 0.7719 (t) REVERT: B 229 MET cc_start: 0.8706 (pmm) cc_final: 0.8444 (pmm) REVERT: B 230 THR cc_start: 0.7238 (m) cc_final: 0.6949 (m) REVERT: B 235 GLN cc_start: 0.9172 (tt0) cc_final: 0.8584 (tm-30) REVERT: H 19 LYS cc_start: 0.8670 (tptt) cc_final: 0.8404 (tptp) REVERT: H 20 VAL cc_start: 0.8792 (t) cc_final: 0.8326 (t) REVERT: H 46 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7712 (mm-30) REVERT: H 80 MET cc_start: 0.8183 (mtp) cc_final: 0.7895 (mtp) REVERT: K 48 ILE cc_start: 0.7787 (tp) cc_final: 0.7284 (tp) REVERT: K 70 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8872 (mm-30) REVERT: K 90 GLN cc_start: 0.8324 (tt0) cc_final: 0.7863 (tt0) REVERT: K 97 THR cc_start: 0.7963 (t) cc_final: 0.7459 (p) REVERT: C 77 THR cc_start: 0.7872 (p) cc_final: 0.7234 (t) REVERT: C 229 MET cc_start: 0.8659 (pmm) cc_final: 0.8370 (pmm) REVERT: C 230 THR cc_start: 0.7282 (m) cc_final: 0.6963 (m) REVERT: C 235 GLN cc_start: 0.9230 (tt0) cc_final: 0.8754 (tm-30) REVERT: I 19 LYS cc_start: 0.8917 (tppt) cc_final: 0.8484 (tptp) REVERT: I 64 GLN cc_start: 0.8487 (mt0) cc_final: 0.8020 (tp40) REVERT: I 80 MET cc_start: 0.8851 (ptp) cc_final: 0.8595 (mtm) REVERT: L 39 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8621 (mmpt) REVERT: L 70 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9161 (mm-30) REVERT: L 90 GLN cc_start: 0.8254 (tt0) cc_final: 0.7832 (tt0) REVERT: L 97 THR cc_start: 0.7889 (t) cc_final: 0.7322 (p) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.2652 time to fit residues: 108.4253 Evaluate side-chains 203 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS H 79 HIS E 516 HIS ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13473 Z= 0.275 Angle : 0.753 11.969 18300 Z= 0.388 Chirality : 0.049 0.249 2106 Planarity : 0.005 0.049 2310 Dihedral : 8.297 56.363 2268 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.21 % Allowed : 1.00 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.45 (0.20), residues: 1614 helix: 0.59 (0.35), residues: 216 sheet: -0.90 (0.22), residues: 504 loop : -1.38 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 35 HIS 0.008 0.002 HIS H 100C PHE 0.018 0.002 PHE I 29 TYR 0.025 0.002 TYR F 534 ARG 0.008 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 1.517 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: A 77 THR cc_start: 0.8077 (p) cc_final: 0.7532 (t) REVERT: A 122 LEU cc_start: 0.9152 (mm) cc_final: 0.8645 (mm) REVERT: A 172 ARG cc_start: 0.7743 (ptp90) cc_final: 0.7391 (ptp90) REVERT: A 229 MET cc_start: 0.8596 (pmm) cc_final: 0.8351 (pmm) REVERT: A 230 THR cc_start: 0.7320 (m) cc_final: 0.7029 (m) REVERT: A 231 ASN cc_start: 0.8702 (t0) cc_final: 0.7886 (p0) REVERT: A 235 GLN cc_start: 0.9173 (tt0) cc_final: 0.8543 (tm-30) REVERT: G 64 GLN cc_start: 0.8114 (mm110) cc_final: 0.7878 (mm-40) REVERT: G 81 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7454 (tp30) REVERT: G 90 TYR cc_start: 0.8578 (m-10) cc_final: 0.8107 (m-80) REVERT: G 97 ILE cc_start: 0.8100 (pt) cc_final: 0.7780 (mm) REVERT: J 39 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8672 (mmmt) REVERT: J 90 GLN cc_start: 0.8475 (tt0) cc_final: 0.7922 (tt0) REVERT: J 97 THR cc_start: 0.7777 (t) cc_final: 0.7234 (p) REVERT: D 602 HIS cc_start: 0.6943 (t70) cc_final: 0.6004 (m170) REVERT: B 77 THR cc_start: 0.8139 (p) cc_final: 0.7702 (t) REVERT: B 229 MET cc_start: 0.8662 (pmm) cc_final: 0.8391 (pmm) REVERT: B 230 THR cc_start: 0.7229 (m) cc_final: 0.6894 (m) REVERT: B 231 ASN cc_start: 0.8749 (t0) cc_final: 0.8012 (p0) REVERT: B 235 GLN cc_start: 0.9158 (tt0) cc_final: 0.8542 (tm-30) REVERT: H 19 LYS cc_start: 0.8637 (tptt) cc_final: 0.8340 (tptp) REVERT: H 20 VAL cc_start: 0.8746 (t) cc_final: 0.8254 (t) REVERT: H 46 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7555 (mm-30) REVERT: H 52 MET cc_start: 0.8285 (mmm) cc_final: 0.7962 (mmm) REVERT: H 53 ILE cc_start: 0.8120 (tt) cc_final: 0.7826 (pt) REVERT: H 80 MET cc_start: 0.8129 (mtp) cc_final: 0.7737 (mtp) REVERT: K 48 ILE cc_start: 0.7889 (tp) cc_final: 0.7592 (tp) REVERT: K 70 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8902 (mm-30) REVERT: K 90 GLN cc_start: 0.8336 (tt0) cc_final: 0.7707 (tt0) REVERT: K 97 THR cc_start: 0.7931 (t) cc_final: 0.6936 (p) REVERT: C 77 THR cc_start: 0.7879 (p) cc_final: 0.7187 (t) REVERT: C 229 MET cc_start: 0.8580 (pmm) cc_final: 0.8369 (pmm) REVERT: C 235 GLN cc_start: 0.9249 (tt0) cc_final: 0.8554 (tm-30) REVERT: I 19 LYS cc_start: 0.8697 (tppt) cc_final: 0.8495 (tppt) REVERT: I 48 MET cc_start: 0.9164 (mtt) cc_final: 0.8737 (mpp) REVERT: I 52 MET cc_start: 0.8630 (mpp) cc_final: 0.8053 (mpp) REVERT: I 64 GLN cc_start: 0.8442 (mt0) cc_final: 0.7975 (tp40) REVERT: I 80 MET cc_start: 0.8747 (ptp) cc_final: 0.8272 (ptm) REVERT: I 81 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7827 (tp30) REVERT: L 42 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8685 (mp10) REVERT: L 70 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9160 (mm-30) REVERT: L 90 GLN cc_start: 0.8375 (tt0) cc_final: 0.7801 (tt0) REVERT: L 97 THR cc_start: 0.7790 (t) cc_final: 0.6699 (p) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.2617 time to fit residues: 107.6122 Evaluate side-chains 199 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 93 optimal weight: 40.0000 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13473 Z= 0.463 Angle : 0.872 13.081 18300 Z= 0.443 Chirality : 0.052 0.253 2106 Planarity : 0.007 0.142 2310 Dihedral : 8.523 54.258 2268 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -1.51 (0.20), residues: 1614 helix: 0.65 (0.35), residues: 195 sheet: -0.99 (0.22), residues: 513 loop : -1.38 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP I 103 HIS 0.009 0.003 HIS H 100C PHE 0.030 0.003 PHE I 29 TYR 0.032 0.003 TYR I 33 ARG 0.014 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.476 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: A 77 THR cc_start: 0.8280 (p) cc_final: 0.7792 (t) REVERT: A 229 MET cc_start: 0.8675 (pmm) cc_final: 0.8445 (pmm) REVERT: A 230 THR cc_start: 0.7608 (m) cc_final: 0.7324 (m) REVERT: A 231 ASN cc_start: 0.8604 (t0) cc_final: 0.8173 (p0) REVERT: A 235 GLN cc_start: 0.9198 (tt0) cc_final: 0.8560 (tm-30) REVERT: G 19 LYS cc_start: 0.8784 (tptt) cc_final: 0.8511 (tptp) REVERT: G 29 PHE cc_start: 0.6838 (m-10) cc_final: 0.6463 (m-80) REVERT: G 35 ILE cc_start: 0.8701 (mm) cc_final: 0.8456 (tp) REVERT: G 48 MET cc_start: 0.9235 (mtt) cc_final: 0.8744 (mpp) REVERT: G 64 GLN cc_start: 0.8252 (mm110) cc_final: 0.7999 (mm-40) REVERT: G 97 ILE cc_start: 0.8241 (pt) cc_final: 0.7960 (mm) REVERT: J 90 GLN cc_start: 0.8568 (tt0) cc_final: 0.7999 (tt0) REVERT: J 97 THR cc_start: 0.7940 (t) cc_final: 0.7412 (p) REVERT: D 602 HIS cc_start: 0.6702 (t-90) cc_final: 0.6068 (m170) REVERT: B 229 MET cc_start: 0.8724 (pmm) cc_final: 0.8500 (pmm) REVERT: B 230 THR cc_start: 0.7495 (m) cc_final: 0.7178 (m) REVERT: B 231 ASN cc_start: 0.8654 (t0) cc_final: 0.8249 (p0) REVERT: B 235 GLN cc_start: 0.9134 (tt0) cc_final: 0.8637 (tt0) REVERT: H 20 VAL cc_start: 0.8793 (t) cc_final: 0.8331 (t) REVERT: H 52 MET cc_start: 0.8310 (mmm) cc_final: 0.8075 (mmm) REVERT: H 80 MET cc_start: 0.8159 (mtp) cc_final: 0.7808 (mtp) REVERT: K 18 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7041 (ttp80) REVERT: K 42 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8445 (mm110) REVERT: K 48 ILE cc_start: 0.7835 (tp) cc_final: 0.7296 (tp) REVERT: K 70 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8855 (mm-30) REVERT: K 90 GLN cc_start: 0.8485 (tt0) cc_final: 0.7713 (tt0) REVERT: K 97 THR cc_start: 0.8020 (t) cc_final: 0.6924 (p) REVERT: E 517 TYR cc_start: 0.8318 (p90) cc_final: 0.7990 (p90) REVERT: C 55 ASP cc_start: 0.7615 (m-30) cc_final: 0.7396 (m-30) REVERT: C 229 MET cc_start: 0.8685 (pmm) cc_final: 0.8437 (pmm) REVERT: C 231 ASN cc_start: 0.8814 (t0) cc_final: 0.8048 (p0) REVERT: C 235 GLN cc_start: 0.9193 (tt0) cc_final: 0.8577 (tm-30) REVERT: I 48 MET cc_start: 0.9237 (mtt) cc_final: 0.8615 (mpp) REVERT: I 52 MET cc_start: 0.8526 (mpp) cc_final: 0.7839 (mpp) REVERT: I 64 GLN cc_start: 0.8531 (mt0) cc_final: 0.8029 (tp40) REVERT: I 80 MET cc_start: 0.8917 (ptp) cc_final: 0.8323 (ptm) REVERT: I 97 ILE cc_start: 0.8807 (tp) cc_final: 0.8505 (tp) REVERT: L 42 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8597 (mm110) REVERT: L 70 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9198 (mm-30) REVERT: L 90 GLN cc_start: 0.8503 (tt0) cc_final: 0.7764 (tt0) REVERT: L 97 THR cc_start: 0.7891 (t) cc_final: 0.6916 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2534 time to fit residues: 93.5013 Evaluate side-chains 187 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN G 64 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13473 Z= 0.244 Angle : 0.748 13.252 18300 Z= 0.380 Chirality : 0.049 0.230 2106 Planarity : 0.006 0.083 2310 Dihedral : 7.838 48.244 2268 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1614 helix: 1.11 (0.36), residues: 198 sheet: -0.95 (0.23), residues: 501 loop : -1.28 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 35 HIS 0.011 0.002 HIS I 100C PHE 0.014 0.002 PHE H 100E TYR 0.032 0.002 TYR F 534 ARG 0.007 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 1.497 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: A 77 THR cc_start: 0.8182 (p) cc_final: 0.7647 (t) REVERT: A 230 THR cc_start: 0.7473 (m) cc_final: 0.7226 (m) REVERT: A 231 ASN cc_start: 0.8776 (t0) cc_final: 0.8155 (p0) REVERT: A 235 GLN cc_start: 0.9171 (tt0) cc_final: 0.8546 (tm-30) REVERT: G 19 LYS cc_start: 0.8845 (tptt) cc_final: 0.8429 (tptp) REVERT: G 35 ILE cc_start: 0.8765 (mm) cc_final: 0.8405 (tp) REVERT: G 48 MET cc_start: 0.9158 (mtt) cc_final: 0.8671 (mpp) REVERT: G 64 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7873 (mm-40) REVERT: J 24 ARG cc_start: 0.7374 (tpt90) cc_final: 0.7101 (tpt90) REVERT: J 90 GLN cc_start: 0.8677 (tt0) cc_final: 0.8273 (tt0) REVERT: J 97 THR cc_start: 0.7802 (t) cc_final: 0.7443 (p) REVERT: D 583 SER cc_start: 0.8125 (m) cc_final: 0.7740 (p) REVERT: D 602 HIS cc_start: 0.6519 (t-90) cc_final: 0.6042 (m170) REVERT: B 229 MET cc_start: 0.8675 (pmm) cc_final: 0.8449 (pmm) REVERT: B 230 THR cc_start: 0.7399 (m) cc_final: 0.7135 (m) REVERT: B 231 ASN cc_start: 0.8764 (t0) cc_final: 0.8251 (p0) REVERT: B 235 GLN cc_start: 0.9142 (tt0) cc_final: 0.8582 (tm-30) REVERT: H 52 MET cc_start: 0.8270 (mmm) cc_final: 0.8060 (mmm) REVERT: H 80 MET cc_start: 0.7965 (mtp) cc_final: 0.7697 (mtp) REVERT: K 48 ILE cc_start: 0.7665 (tp) cc_final: 0.7036 (tp) REVERT: K 70 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8803 (mm-30) REVERT: K 90 GLN cc_start: 0.8449 (tt0) cc_final: 0.7765 (tt0) REVERT: K 97 THR cc_start: 0.8036 (t) cc_final: 0.7166 (p) REVERT: E 517 TYR cc_start: 0.7931 (p90) cc_final: 0.7651 (p90) REVERT: E 583 SER cc_start: 0.8163 (m) cc_final: 0.7937 (p) REVERT: C 54 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7314 (ttp-110) REVERT: C 55 ASP cc_start: 0.7391 (m-30) cc_final: 0.6914 (m-30) REVERT: C 229 MET cc_start: 0.8596 (pmm) cc_final: 0.8383 (pmm) REVERT: C 231 ASN cc_start: 0.8811 (t0) cc_final: 0.7993 (p0) REVERT: C 235 GLN cc_start: 0.9244 (tt0) cc_final: 0.8539 (tm-30) REVERT: I 48 MET cc_start: 0.9245 (mtt) cc_final: 0.8563 (mpp) REVERT: I 64 GLN cc_start: 0.8527 (mt0) cc_final: 0.8064 (tp40) REVERT: I 81 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7685 (tp30) REVERT: L 42 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8616 (mm110) REVERT: L 53 THR cc_start: 0.8692 (m) cc_final: 0.8486 (p) REVERT: L 73 LEU cc_start: 0.8629 (tp) cc_final: 0.7240 (tp) REVERT: L 90 GLN cc_start: 0.8495 (tt0) cc_final: 0.7922 (tt0) REVERT: L 97 THR cc_start: 0.7815 (t) cc_final: 0.6866 (p) REVERT: F 583 SER cc_start: 0.8024 (m) cc_final: 0.7637 (p) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2605 time to fit residues: 97.3033 Evaluate side-chains 189 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 chunk 151 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.8003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13473 Z= 0.341 Angle : 0.796 14.121 18300 Z= 0.404 Chirality : 0.050 0.213 2106 Planarity : 0.006 0.066 2310 Dihedral : 7.893 50.837 2268 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1614 helix: 0.86 (0.35), residues: 198 sheet: -1.06 (0.22), residues: 516 loop : -1.34 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP I 103 HIS 0.011 0.002 HIS I 100C PHE 0.033 0.002 PHE I 29 TYR 0.029 0.002 TYR D 534 ARG 0.012 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.376 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: A 77 THR cc_start: 0.8272 (p) cc_final: 0.7762 (t) REVERT: A 230 THR cc_start: 0.7650 (m) cc_final: 0.7407 (m) REVERT: A 235 GLN cc_start: 0.9179 (tt0) cc_final: 0.8584 (tm-30) REVERT: G 19 LYS cc_start: 0.8726 (tptt) cc_final: 0.8295 (tptp) REVERT: G 35 ILE cc_start: 0.8716 (mm) cc_final: 0.8497 (tp) REVERT: G 48 MET cc_start: 0.9251 (mtt) cc_final: 0.8769 (mpp) REVERT: G 64 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7937 (mm-40) REVERT: G 90 TYR cc_start: 0.8659 (m-80) cc_final: 0.8415 (m-80) REVERT: J 18 ARG cc_start: 0.7327 (ttp80) cc_final: 0.6670 (ttp80) REVERT: J 24 ARG cc_start: 0.7429 (tpt90) cc_final: 0.7186 (tpt90) REVERT: J 90 GLN cc_start: 0.8749 (tt0) cc_final: 0.8304 (tt0) REVERT: J 97 THR cc_start: 0.7873 (t) cc_final: 0.7445 (p) REVERT: D 583 SER cc_start: 0.8168 (m) cc_final: 0.7794 (p) REVERT: B 230 THR cc_start: 0.7591 (m) cc_final: 0.7290 (m) REVERT: B 231 ASN cc_start: 0.8780 (t0) cc_final: 0.8315 (p0) REVERT: B 235 GLN cc_start: 0.9133 (tt0) cc_final: 0.8677 (tt0) REVERT: H 19 LYS cc_start: 0.8708 (tptt) cc_final: 0.8462 (tptp) REVERT: H 20 VAL cc_start: 0.8712 (t) cc_final: 0.8426 (t) REVERT: H 35 ILE cc_start: 0.8834 (mm) cc_final: 0.8595 (tp) REVERT: H 52 MET cc_start: 0.8283 (mmm) cc_final: 0.8032 (mmm) REVERT: H 64 GLN cc_start: 0.8722 (mt0) cc_final: 0.8158 (tp40) REVERT: H 80 MET cc_start: 0.8127 (mtp) cc_final: 0.7750 (mtp) REVERT: K 48 ILE cc_start: 0.7704 (tp) cc_final: 0.7091 (tp) REVERT: K 71 PHE cc_start: 0.8995 (m-10) cc_final: 0.8551 (m-10) REVERT: K 90 GLN cc_start: 0.8576 (tt0) cc_final: 0.7801 (tt0) REVERT: K 97 THR cc_start: 0.8014 (t) cc_final: 0.7150 (p) REVERT: E 517 TYR cc_start: 0.8275 (p90) cc_final: 0.7984 (p90) REVERT: E 583 SER cc_start: 0.8342 (m) cc_final: 0.8095 (p) REVERT: C 55 ASP cc_start: 0.7487 (m-30) cc_final: 0.7278 (m-30) REVERT: C 231 ASN cc_start: 0.8763 (t0) cc_final: 0.8074 (p0) REVERT: C 235 GLN cc_start: 0.9260 (tt0) cc_final: 0.8532 (tm-30) REVERT: I 20 VAL cc_start: 0.8530 (t) cc_final: 0.7997 (t) REVERT: I 48 MET cc_start: 0.9311 (mtt) cc_final: 0.8644 (mpp) REVERT: I 64 GLN cc_start: 0.8526 (mt0) cc_final: 0.8032 (tp40) REVERT: I 81 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7475 (tp30) REVERT: L 13 VAL cc_start: 0.6930 (t) cc_final: 0.6289 (t) REVERT: L 70 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8769 (mm-30) REVERT: L 90 GLN cc_start: 0.8531 (tt0) cc_final: 0.7803 (tt0) REVERT: L 97 THR cc_start: 0.7869 (t) cc_final: 0.6912 (p) REVERT: F 583 SER cc_start: 0.8101 (m) cc_final: 0.7750 (p) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2477 time to fit residues: 90.8880 Evaluate side-chains 186 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13473 Z= 0.241 Angle : 0.753 13.663 18300 Z= 0.378 Chirality : 0.048 0.227 2106 Planarity : 0.006 0.070 2310 Dihedral : 7.438 57.878 2268 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.21), residues: 1614 helix: 1.15 (0.36), residues: 198 sheet: -1.10 (0.22), residues: 516 loop : -1.26 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP K 35 HIS 0.009 0.002 HIS H 100C PHE 0.021 0.002 PHE I 29 TYR 0.026 0.002 TYR F 534 ARG 0.010 0.001 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.418 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: A 69 ASN cc_start: 0.8353 (m-40) cc_final: 0.7794 (m-40) REVERT: A 77 THR cc_start: 0.8213 (p) cc_final: 0.7691 (t) REVERT: A 230 THR cc_start: 0.7577 (m) cc_final: 0.7272 (m) REVERT: A 235 GLN cc_start: 0.9162 (tt0) cc_final: 0.8521 (tm-30) REVERT: G 19 LYS cc_start: 0.8698 (tptt) cc_final: 0.8259 (tptp) REVERT: G 35 ILE cc_start: 0.8782 (mm) cc_final: 0.8520 (tp) REVERT: G 48 MET cc_start: 0.9231 (mtt) cc_final: 0.8685 (mpp) REVERT: G 64 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7898 (mm-40) REVERT: G 90 TYR cc_start: 0.8612 (m-80) cc_final: 0.8404 (m-80) REVERT: J 18 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7050 (ttp80) REVERT: J 90 GLN cc_start: 0.8672 (tt0) cc_final: 0.8239 (tt0) REVERT: J 97 THR cc_start: 0.7843 (t) cc_final: 0.7457 (p) REVERT: D 583 SER cc_start: 0.8023 (m) cc_final: 0.7804 (p) REVERT: B 77 THR cc_start: 0.8386 (p) cc_final: 0.8016 (t) REVERT: B 229 MET cc_start: 0.8636 (pmm) cc_final: 0.8305 (pmm) REVERT: B 230 THR cc_start: 0.7469 (m) cc_final: 0.7181 (m) REVERT: B 231 ASN cc_start: 0.8788 (t0) cc_final: 0.8371 (p0) REVERT: B 235 GLN cc_start: 0.9221 (tt0) cc_final: 0.8511 (tm-30) REVERT: H 19 LYS cc_start: 0.8754 (tptt) cc_final: 0.8489 (tptp) REVERT: H 20 VAL cc_start: 0.8694 (t) cc_final: 0.8402 (t) REVERT: H 48 MET cc_start: 0.8910 (mtt) cc_final: 0.8649 (mpp) REVERT: H 52 MET cc_start: 0.8276 (mmm) cc_final: 0.8022 (mmm) REVERT: H 64 GLN cc_start: 0.8723 (mt0) cc_final: 0.8155 (tp40) REVERT: H 80 MET cc_start: 0.8159 (mtp) cc_final: 0.7934 (mtp) REVERT: K 48 ILE cc_start: 0.7635 (tp) cc_final: 0.7145 (tp) REVERT: K 70 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8857 (mm-30) REVERT: K 71 PHE cc_start: 0.8832 (m-10) cc_final: 0.8352 (m-10) REVERT: K 90 GLN cc_start: 0.8540 (tt0) cc_final: 0.7904 (tt0) REVERT: K 97 THR cc_start: 0.8050 (t) cc_final: 0.7249 (p) REVERT: E 517 TYR cc_start: 0.8161 (p90) cc_final: 0.7912 (p90) REVERT: E 583 SER cc_start: 0.8220 (m) cc_final: 0.7997 (p) REVERT: C 55 ASP cc_start: 0.7440 (m-30) cc_final: 0.7193 (m-30) REVERT: C 231 ASN cc_start: 0.8647 (t0) cc_final: 0.8081 (p0) REVERT: C 235 GLN cc_start: 0.9236 (tt0) cc_final: 0.8491 (tm-30) REVERT: I 48 MET cc_start: 0.9288 (mtt) cc_final: 0.8498 (mpp) REVERT: I 64 GLN cc_start: 0.8459 (mt0) cc_final: 0.8028 (tp40) REVERT: I 81 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7390 (tp30) REVERT: L 70 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8744 (mm-30) REVERT: L 90 GLN cc_start: 0.8458 (tt0) cc_final: 0.7803 (tt0) REVERT: L 97 THR cc_start: 0.7810 (t) cc_final: 0.6933 (p) REVERT: F 583 SER cc_start: 0.8011 (m) cc_final: 0.7779 (p) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.2417 time to fit residues: 91.3803 Evaluate side-chains 191 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.116641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087129 restraints weight = 32033.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.087562 restraints weight = 18047.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088330 restraints weight = 13283.348| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.8410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13473 Z= 0.333 Angle : 0.780 12.958 18300 Z= 0.399 Chirality : 0.048 0.275 2106 Planarity : 0.006 0.061 2310 Dihedral : 6.880 50.772 2268 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1614 helix: 1.06 (0.36), residues: 195 sheet: -1.25 (0.21), residues: 549 loop : -1.28 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 103 HIS 0.011 0.002 HIS I 100C PHE 0.032 0.002 PHE I 29 TYR 0.040 0.003 TYR L 36 ARG 0.007 0.001 ARG B 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.07 seconds wall clock time: 52 minutes 46.66 seconds (3166.66 seconds total)