Starting phenix.real_space_refine on Fri Jan 19 21:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/01_2024/6dzl_8935.pdb" } resolution = 4.14 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= 0.000 sd= 0.002 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 42 5.16 5 C 8040 2.51 5 N 2100 2.21 5 O 2511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ASP 50": "OD1" <-> "OD2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 97": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12693 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1664 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1664 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "E" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "C" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1664 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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: "B" 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: "C" 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 Time building chain proxies: 7.04, per 1000 atoms: 0.55 Number of scatterers: 12693 At special positions: 0 Unit cell: (136.85, 139.15, 85.1, 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 42 16.00 O 2511 8.00 N 2100 7.00 C 8040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN P 4 " - " MAN P 5 " " MAN R 4 " - " MAN R 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " 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 403 " - " ASN A 40 " " NAG A 404 " - " ASN A 238 " " NAG B 403 " - " ASN B 40 " " NAG B 404 " - " ASN B 238 " " NAG C 403 " - " ASN C 40 " " NAG C 404 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 2.9 seconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 15.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.726A pdb=" N THR A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 556 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.666A 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 'J' and resid 80 through 84 removed outlier: 3.765A pdb=" N ALA J 84 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.725A pdb=" N THR B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 556 " --> pdb=" O ASP E 552 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.666A 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 'K' and resid 80 through 84 removed outlier: 3.764A pdb=" N ALA K 84 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.727A pdb=" N THR C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE F 555 " --> pdb=" O GLN F 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS F 556 " --> pdb=" O ASP F 552 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.765A pdb=" N ALA L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.936A pdb=" N VAL A 37 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 44 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.506A pdb=" N VAL A 97 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 114 removed outlier: 7.047A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.532A pdb=" N THR A 223 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.489A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 17 through 20 removed outlier: 3.567A pdb=" N SER G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.671A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 93 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 39 removed outlier: 3.937A pdb=" N VAL B 37 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 44 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 64 through 69 Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.506A pdb=" N VAL B 97 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 114 removed outlier: 7.046A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.531A pdb=" N THR B 223 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 515 through 516 Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.311A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.568A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.671A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.936A pdb=" N VAL C 37 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 44 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 64 through 69 Processing sheet with id=AC9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.505A pdb=" N VAL C 97 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 108 through 114 removed outlier: 7.046A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.532A pdb=" N THR C 223 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 515 through 516 Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 17 through 20 removed outlier: 3.568A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.670A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA I 93 " --> pdb=" O SER I 35 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.13 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4020 1.34 - 1.46: 3431 1.46 - 1.58: 5485 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 12987 Sorted by residual: bond pdb=" C PHE A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.336 1.309 0.026 1.23e-02 6.61e+03 4.64e+00 bond pdb=" C PHE C 132 " pdb=" N PRO C 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.12e+00 bond pdb=" C PHE B 132 " pdb=" N PRO B 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.08e+00 bond pdb=" CA ARG C 134 " pdb=" CB ARG C 134 " ideal model delta sigma weight residual 1.527 1.480 0.047 2.48e-02 1.63e+03 3.61e+00 bond pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta sigma weight residual 1.533 1.490 0.043 2.29e-02 1.91e+03 3.49e+00 ... (remaining 12982 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.99: 263 105.99 - 113.12: 7265 113.12 - 120.24: 4269 120.24 - 127.37: 5690 127.37 - 134.49: 162 Bond angle restraints: 17649 Sorted by residual: angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.10 109.66 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.10 109.73 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N ALA J 51 " pdb=" CA ALA J 51 " pdb=" CB ALA J 51 " ideal model delta sigma weight residual 114.10 109.75 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N GLY D 524 " pdb=" CA GLY D 524 " pdb=" C GLY D 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 angle pdb=" N GLY F 524 " pdb=" CA GLY F 524 " pdb=" C GLY F 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 ... (remaining 17644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 7605 22.65 - 45.29: 186 45.29 - 67.94: 6 67.94 - 90.58: 18 90.58 - 113.23: 12 Dihedral angle restraints: 7827 sinusoidal: 3291 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LEU A 51 " pdb=" C LEU A 51 " pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 51 " pdb=" C LEU C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N VAL B 52 " pdb=" CA VAL B 52 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 2028 0.317 - 0.634: 3 0.634 - 0.951: 0 0.951 - 1.268: 0 1.268 - 1.585: 3 Chirality restraints: 2034 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 238 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.81 -1.59 2.00e-01 2.50e+01 6.28e+01 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 238 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 238 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.19e+01 ... (remaining 2031 not shown) Planarity restraints: 2232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.065 2.00e-02 2.50e+03 7.76e-02 7.53e+01 pdb=" CG ASN C 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.129 2.00e-02 2.50e+03 pdb=" C1 NAG C 404 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.064 2.00e-02 2.50e+03 7.74e-02 7.49e+01 pdb=" CG ASN A 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.129 2.00e-02 2.50e+03 pdb=" C1 NAG A 404 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 238 " -0.064 2.00e-02 2.50e+03 7.70e-02 7.41e+01 pdb=" CG ASN B 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 238 " 0.128 2.00e-02 2.50e+03 pdb=" C1 NAG B 404 " -0.093 2.00e-02 2.50e+03 ... (remaining 2229 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 280 2.63 - 3.20: 12522 3.20 - 3.77: 19679 3.77 - 4.33: 26990 4.33 - 4.90: 43975 Nonbonded interactions: 103446 Sorted by model distance: nonbonded pdb=" O SER K 49 " pdb=" OD2 ASP K 50 " model vdw 2.069 3.040 nonbonded pdb=" O SER J 49 " pdb=" OD2 ASP J 50 " model vdw 2.069 3.040 nonbonded pdb=" O SER L 49 " pdb=" OD2 ASP L 50 " model vdw 2.070 3.040 nonbonded pdb=" OG SER K 52 " pdb=" O6 MAN P 5 " model vdw 2.246 2.440 nonbonded pdb=" OG SER J 52 " pdb=" O6 MAN N 5 " model vdw 2.246 2.440 ... (remaining 103441 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 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' 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: 5.140 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: 13.650 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 46.620 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.012 0.073 12987 Z= 0.762 Angle : 0.954 8.629 17649 Z= 0.501 Chirality : 0.080 1.585 2034 Planarity : 0.006 0.050 2220 Dihedral : 11.461 113.229 4896 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.57 (0.18), residues: 1557 helix: -1.99 (0.33), residues: 177 sheet: -3.80 (0.16), residues: 468 loop : -2.87 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 47 HIS 0.004 0.001 HIS I 100D PHE 0.017 0.003 PHE K 71 TYR 0.017 0.003 TYR A 109 ARG 0.010 0.001 ARG F 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.325 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.9802 (mttt) cc_final: 0.9585 (mttp) REVERT: D 591 ASP cc_start: 0.8916 (m-30) cc_final: 0.8649 (m-30) REVERT: G 39 GLN cc_start: 0.9536 (tt0) cc_final: 0.9237 (tt0) REVERT: H 39 GLN cc_start: 0.9558 (tt0) cc_final: 0.9249 (tt0) REVERT: C 84 LYS cc_start: 0.9776 (mttt) cc_final: 0.9551 (mttp) REVERT: I 39 GLN cc_start: 0.9471 (tt0) cc_final: 0.9140 (tt0) outliers start: 3 outliers final: 0 residues processed: 242 average time/residue: 0.3697 time to fit residues: 117.9065 Evaluate side-chains 94 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN G 13 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 13 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS L 37 GLN I 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12987 Z= 0.193 Angle : 0.647 8.005 17649 Z= 0.328 Chirality : 0.046 0.324 2034 Planarity : 0.005 0.038 2220 Dihedral : 10.374 78.334 2166 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.44 (0.20), residues: 1557 helix: -1.09 (0.35), residues: 198 sheet: -2.76 (0.20), residues: 426 loop : -2.37 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 597 HIS 0.002 0.001 HIS E 549 PHE 0.015 0.001 PHE D 572 TYR 0.013 0.002 TYR B 261 ARG 0.003 0.000 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.513 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: A 84 LYS cc_start: 0.9758 (mttt) cc_final: 0.9515 (mttp) REVERT: G 39 GLN cc_start: 0.9590 (tt0) cc_final: 0.9084 (tt0) REVERT: B 84 LYS cc_start: 0.9777 (mttt) cc_final: 0.9548 (mttp) REVERT: H 39 GLN cc_start: 0.9604 (tt0) cc_final: 0.9282 (tt0) REVERT: H 73 ASN cc_start: 0.9294 (p0) cc_final: 0.8692 (m-40) REVERT: C 69 ASN cc_start: 0.8914 (m-40) cc_final: 0.8530 (m110) REVERT: C 84 LYS cc_start: 0.9747 (mttt) cc_final: 0.9535 (mttp) REVERT: L 74 THR cc_start: 0.9428 (t) cc_final: 0.9119 (t) REVERT: I 39 GLN cc_start: 0.9522 (tt0) cc_final: 0.9079 (tt0) REVERT: I 105 GLN cc_start: 0.8774 (mp10) cc_final: 0.8489 (mp10) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2900 time to fit residues: 62.1141 Evaluate side-chains 95 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 115 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12987 Z= 0.217 Angle : 0.595 7.443 17649 Z= 0.299 Chirality : 0.044 0.302 2034 Planarity : 0.004 0.040 2220 Dihedral : 9.142 67.550 2166 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.21), residues: 1557 helix: -0.08 (0.40), residues: 180 sheet: -2.17 (0.22), residues: 408 loop : -1.98 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 531 HIS 0.010 0.001 HIS F 516 PHE 0.009 0.001 PHE D 572 TYR 0.012 0.001 TYR A 261 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.559 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 84 LYS cc_start: 0.9761 (mttt) cc_final: 0.9517 (mtmm) REVERT: A 127 ASP cc_start: 0.8810 (t70) cc_final: 0.8479 (t0) REVERT: J 27 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8248 (tm-30) REVERT: J 83 PHE cc_start: 0.8381 (m-80) cc_final: 0.8005 (m-80) REVERT: G 39 GLN cc_start: 0.9617 (tt0) cc_final: 0.9067 (tt0) REVERT: G 82 MET cc_start: 0.8994 (mpp) cc_final: 0.8604 (mpp) REVERT: B 69 ASN cc_start: 0.8981 (m-40) cc_final: 0.8650 (m110) REVERT: B 84 LYS cc_start: 0.9781 (mttt) cc_final: 0.9567 (mtmm) REVERT: E 552 ASP cc_start: 0.8552 (m-30) cc_final: 0.8076 (m-30) REVERT: H 34 MET cc_start: 0.9280 (mmp) cc_final: 0.9013 (mmm) REVERT: H 39 GLN cc_start: 0.9637 (tt0) cc_final: 0.9297 (tt0) REVERT: H 73 ASN cc_start: 0.9110 (p0) cc_final: 0.8691 (m-40) REVERT: H 82 MET cc_start: 0.8985 (mpp) cc_final: 0.8550 (mpp) REVERT: C 69 ASN cc_start: 0.8810 (m-40) cc_final: 0.8395 (m110) REVERT: C 84 LYS cc_start: 0.9756 (mttt) cc_final: 0.9532 (mtmm) REVERT: I 39 GLN cc_start: 0.9519 (tt0) cc_final: 0.9059 (tt0) REVERT: I 82 MET cc_start: 0.9041 (mpp) cc_final: 0.8674 (mpp) REVERT: I 105 GLN cc_start: 0.8801 (mp10) cc_final: 0.8534 (mp10) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2929 time to fit residues: 54.7768 Evaluate side-chains 92 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12987 Z= 0.214 Angle : 0.576 7.059 17649 Z= 0.286 Chirality : 0.043 0.284 2034 Planarity : 0.004 0.051 2220 Dihedral : 8.403 59.675 2166 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1557 helix: -0.11 (0.37), residues: 201 sheet: -2.17 (0.23), residues: 393 loop : -1.71 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 531 HIS 0.009 0.001 HIS F 516 PHE 0.009 0.001 PHE E 582 TYR 0.012 0.001 TYR C 261 ARG 0.002 0.000 ARG G 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.364 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 84 LYS cc_start: 0.9761 (mttt) cc_final: 0.9525 (mtmm) REVERT: A 127 ASP cc_start: 0.8855 (t70) cc_final: 0.8581 (t0) REVERT: D 552 ASP cc_start: 0.8490 (m-30) cc_final: 0.7768 (m-30) REVERT: J 74 THR cc_start: 0.9515 (t) cc_final: 0.9282 (t) REVERT: J 83 PHE cc_start: 0.8424 (m-80) cc_final: 0.8203 (m-80) REVERT: G 39 GLN cc_start: 0.9608 (tt0) cc_final: 0.9027 (tt0) REVERT: G 82 MET cc_start: 0.9085 (mpp) cc_final: 0.8838 (mpp) REVERT: B 69 ASN cc_start: 0.8988 (m-40) cc_final: 0.8654 (m110) REVERT: B 84 LYS cc_start: 0.9769 (mttt) cc_final: 0.9535 (mtmm) REVERT: E 552 ASP cc_start: 0.8554 (m-30) cc_final: 0.7800 (m-30) REVERT: K 74 THR cc_start: 0.9467 (t) cc_final: 0.9074 (t) REVERT: H 34 MET cc_start: 0.9351 (mmp) cc_final: 0.9115 (mmm) REVERT: H 73 ASN cc_start: 0.9116 (p0) cc_final: 0.8834 (m110) REVERT: H 82 MET cc_start: 0.9033 (mpp) cc_final: 0.8743 (mpp) REVERT: C 69 ASN cc_start: 0.8852 (m-40) cc_final: 0.8448 (m110) REVERT: F 552 ASP cc_start: 0.8596 (m-30) cc_final: 0.8161 (m-30) REVERT: I 82 MET cc_start: 0.9070 (mpp) cc_final: 0.8816 (mpp) REVERT: I 83 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8279 (mtm180) REVERT: I 105 GLN cc_start: 0.8723 (mp10) cc_final: 0.8473 (mp10) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2897 time to fit residues: 49.6525 Evaluate side-chains 83 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12987 Z= 0.261 Angle : 0.600 7.497 17649 Z= 0.295 Chirality : 0.044 0.287 2034 Planarity : 0.004 0.057 2220 Dihedral : 7.747 50.650 2166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1557 helix: 0.24 (0.37), residues: 204 sheet: -2.19 (0.21), residues: 480 loop : -1.44 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 99 HIS 0.009 0.001 HIS F 516 PHE 0.014 0.001 PHE B 132 TYR 0.014 0.001 TYR H 90 ARG 0.003 0.000 ARG I 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.449 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 127 ASP cc_start: 0.8884 (t70) cc_final: 0.8523 (t0) REVERT: D 552 ASP cc_start: 0.8592 (m-30) cc_final: 0.8077 (m-30) REVERT: J 83 PHE cc_start: 0.8623 (m-80) cc_final: 0.8406 (m-80) REVERT: G 82 MET cc_start: 0.9026 (mpp) cc_final: 0.8822 (mpp) REVERT: B 69 ASN cc_start: 0.9025 (m-40) cc_final: 0.8657 (m110) REVERT: B 260 ILE cc_start: 0.8582 (mm) cc_final: 0.8314 (tp) REVERT: E 552 ASP cc_start: 0.8673 (m-30) cc_final: 0.7957 (m-30) REVERT: H 34 MET cc_start: 0.9387 (mmp) cc_final: 0.9186 (mmm) REVERT: H 73 ASN cc_start: 0.9118 (p0) cc_final: 0.8610 (m-40) REVERT: C 69 ASN cc_start: 0.9009 (m-40) cc_final: 0.8617 (m110) REVERT: C 260 ILE cc_start: 0.8547 (mm) cc_final: 0.8266 (tp) REVERT: F 552 ASP cc_start: 0.8572 (m-30) cc_final: 0.8054 (m-30) REVERT: L 83 PHE cc_start: 0.8834 (m-80) cc_final: 0.8570 (m-80) REVERT: I 82 MET cc_start: 0.9025 (mpp) cc_final: 0.8817 (mpp) REVERT: I 83 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8298 (mtm180) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3050 time to fit residues: 47.5288 Evaluate side-chains 77 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 148 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 0.0010 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12987 Z= 0.169 Angle : 0.550 9.525 17649 Z= 0.269 Chirality : 0.043 0.251 2034 Planarity : 0.004 0.054 2220 Dihedral : 7.291 51.289 2166 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.97 (0.21), residues: 1557 helix: 0.52 (0.38), residues: 204 sheet: -1.85 (0.22), residues: 444 loop : -1.44 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS F 516 PHE 0.011 0.001 PHE A 234 TYR 0.010 0.001 TYR C 261 ARG 0.006 0.000 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.433 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 127 ASP cc_start: 0.8905 (t70) cc_final: 0.8552 (t0) REVERT: D 552 ASP cc_start: 0.8600 (m-30) cc_final: 0.8098 (m-30) REVERT: D 578 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8064 (pt0) REVERT: J 83 PHE cc_start: 0.8679 (m-80) cc_final: 0.8413 (m-80) REVERT: B 69 ASN cc_start: 0.8998 (m-40) cc_final: 0.8664 (m110) REVERT: B 260 ILE cc_start: 0.8641 (mm) cc_final: 0.8329 (tp) REVERT: E 552 ASP cc_start: 0.8537 (m-30) cc_final: 0.7803 (m-30) REVERT: K 75 ILE cc_start: 0.9189 (mp) cc_final: 0.8945 (tt) REVERT: H 34 MET cc_start: 0.9421 (mmp) cc_final: 0.9112 (mmm) REVERT: H 73 ASN cc_start: 0.9120 (p0) cc_final: 0.8598 (m-40) REVERT: H 83 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8344 (mtm180) REVERT: C 69 ASN cc_start: 0.8991 (m-40) cc_final: 0.8616 (m110) REVERT: C 260 ILE cc_start: 0.8508 (mm) cc_final: 0.8254 (tp) REVERT: F 552 ASP cc_start: 0.8580 (m-30) cc_final: 0.8175 (m-30) REVERT: L 18 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8580 (ttp80) REVERT: L 83 PHE cc_start: 0.8721 (m-80) cc_final: 0.8491 (m-80) REVERT: I 83 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8278 (mtm180) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3005 time to fit residues: 44.0660 Evaluate side-chains 77 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 overall best weight: 0.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12987 Z= 0.128 Angle : 0.521 7.960 17649 Z= 0.254 Chirality : 0.043 0.228 2034 Planarity : 0.004 0.053 2220 Dihedral : 6.819 59.968 2166 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.77 (0.21), residues: 1557 helix: 0.60 (0.38), residues: 204 sheet: -1.47 (0.23), residues: 426 loop : -1.44 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.004 0.001 HIS F 516 PHE 0.010 0.001 PHE A 234 TYR 0.008 0.001 TYR C 261 ARG 0.010 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.454 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 69 ASN cc_start: 0.8890 (m-40) cc_final: 0.8550 (m110) REVERT: A 114 LYS cc_start: 0.9080 (mtpp) cc_final: 0.8872 (ttmm) REVERT: A 127 ASP cc_start: 0.8896 (t70) cc_final: 0.8562 (t0) REVERT: D 552 ASP cc_start: 0.8485 (m-30) cc_final: 0.8004 (m-30) REVERT: D 578 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7919 (pt0) REVERT: B 69 ASN cc_start: 0.8951 (m-40) cc_final: 0.8688 (m110) REVERT: B 260 ILE cc_start: 0.8613 (mm) cc_final: 0.8377 (tp) REVERT: E 552 ASP cc_start: 0.8516 (m-30) cc_final: 0.7783 (m-30) REVERT: H 34 MET cc_start: 0.9443 (mmp) cc_final: 0.9060 (mmm) REVERT: H 73 ASN cc_start: 0.9128 (p0) cc_final: 0.8612 (m-40) REVERT: H 83 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8314 (mtm180) REVERT: C 69 ASN cc_start: 0.9007 (m-40) cc_final: 0.8676 (m110) REVERT: C 260 ILE cc_start: 0.8486 (mm) cc_final: 0.8260 (tp) REVERT: F 552 ASP cc_start: 0.8518 (m-30) cc_final: 0.8035 (m-30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2909 time to fit residues: 43.4700 Evaluate side-chains 79 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12987 Z= 0.177 Angle : 0.530 7.875 17649 Z= 0.259 Chirality : 0.042 0.232 2034 Planarity : 0.004 0.050 2220 Dihedral : 6.613 59.592 2166 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.86 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.70 (0.22), residues: 1557 helix: 0.65 (0.38), residues: 204 sheet: -1.60 (0.23), residues: 444 loop : -1.28 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.014 0.001 HIS E 516 PHE 0.009 0.001 PHE A 234 TYR 0.009 0.001 TYR J 91 ARG 0.005 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.359 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 84 LYS cc_start: 0.9755 (mttt) cc_final: 0.9526 (mtmm) REVERT: A 127 ASP cc_start: 0.8904 (t70) cc_final: 0.8563 (t0) REVERT: D 552 ASP cc_start: 0.8519 (m-30) cc_final: 0.8063 (m-30) REVERT: B 69 ASN cc_start: 0.8866 (m-40) cc_final: 0.8560 (m110) REVERT: B 260 ILE cc_start: 0.8618 (mm) cc_final: 0.8385 (tp) REVERT: E 552 ASP cc_start: 0.8509 (m-30) cc_final: 0.7760 (m-30) REVERT: H 34 MET cc_start: 0.9450 (mmp) cc_final: 0.9035 (mmm) REVERT: H 73 ASN cc_start: 0.9163 (p0) cc_final: 0.8684 (m-40) REVERT: H 83 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8381 (mtm180) REVERT: C 69 ASN cc_start: 0.9083 (m-40) cc_final: 0.8700 (m110) REVERT: C 260 ILE cc_start: 0.8612 (mm) cc_final: 0.8360 (tp) REVERT: F 552 ASP cc_start: 0.8594 (m-30) cc_final: 0.8123 (m-30) REVERT: I 105 GLN cc_start: 0.8841 (mp10) cc_final: 0.8591 (mp10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2961 time to fit residues: 44.3024 Evaluate side-chains 79 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 141 optimal weight: 0.0770 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.0470 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12987 Z= 0.141 Angle : 0.519 8.424 17649 Z= 0.253 Chirality : 0.042 0.215 2034 Planarity : 0.004 0.051 2220 Dihedral : 6.159 57.518 2166 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.61 (0.22), residues: 1557 helix: 0.64 (0.39), residues: 204 sheet: -1.44 (0.23), residues: 444 loop : -1.25 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.011 0.001 HIS E 516 PHE 0.009 0.001 PHE D 582 TYR 0.008 0.001 TYR J 91 ARG 0.008 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.399 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 69 ASN cc_start: 0.8888 (m-40) cc_final: 0.8479 (m110) REVERT: A 84 LYS cc_start: 0.9749 (mttt) cc_final: 0.9469 (ptpp) REVERT: A 114 LYS cc_start: 0.9348 (ttmm) cc_final: 0.9131 (ttmm) REVERT: A 127 ASP cc_start: 0.8887 (t70) cc_final: 0.8552 (t0) REVERT: D 552 ASP cc_start: 0.8506 (m-30) cc_final: 0.8131 (m-30) REVERT: D 578 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7810 (pt0) REVERT: B 69 ASN cc_start: 0.8827 (m-40) cc_final: 0.8522 (m110) REVERT: B 260 ILE cc_start: 0.8643 (mm) cc_final: 0.8414 (tp) REVERT: E 552 ASP cc_start: 0.8491 (m-30) cc_final: 0.7735 (m-30) REVERT: H 34 MET cc_start: 0.9444 (mmp) cc_final: 0.9006 (mmm) REVERT: H 73 ASN cc_start: 0.9164 (p0) cc_final: 0.8676 (m-40) REVERT: H 83 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8381 (mtm180) REVERT: C 69 ASN cc_start: 0.9076 (m-40) cc_final: 0.8696 (m110) REVERT: C 260 ILE cc_start: 0.8620 (mm) cc_final: 0.8387 (tp) REVERT: F 552 ASP cc_start: 0.8584 (m-30) cc_final: 0.8109 (m-30) REVERT: I 105 GLN cc_start: 0.8808 (mp10) cc_final: 0.8560 (mp10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2743 time to fit residues: 40.8711 Evaluate side-chains 83 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12987 Z= 0.226 Angle : 0.556 7.905 17649 Z= 0.271 Chirality : 0.042 0.227 2034 Planarity : 0.004 0.050 2220 Dihedral : 5.858 46.984 2166 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1557 helix: 0.57 (0.38), residues: 204 sheet: -1.44 (0.23), residues: 444 loop : -1.24 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.012 0.001 HIS E 516 PHE 0.009 0.001 PHE H 100E TYR 0.010 0.001 TYR G 102 ARG 0.007 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.347 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 84 LYS cc_start: 0.9736 (mttt) cc_final: 0.9467 (ptpp) REVERT: A 127 ASP cc_start: 0.8856 (t70) cc_final: 0.8524 (t0) REVERT: D 552 ASP cc_start: 0.8536 (m-30) cc_final: 0.8131 (m-30) REVERT: D 555 ILE cc_start: 0.9518 (mp) cc_final: 0.8886 (tt) REVERT: B 69 ASN cc_start: 0.8927 (m-40) cc_final: 0.8583 (m110) REVERT: B 260 ILE cc_start: 0.8654 (mm) cc_final: 0.8433 (tp) REVERT: E 552 ASP cc_start: 0.8656 (m-30) cc_final: 0.7957 (m-30) REVERT: H 34 MET cc_start: 0.9430 (mmp) cc_final: 0.8856 (mmp) REVERT: H 73 ASN cc_start: 0.9149 (p0) cc_final: 0.8697 (m-40) REVERT: C 69 ASN cc_start: 0.9046 (m-40) cc_final: 0.8537 (m110) REVERT: F 552 ASP cc_start: 0.8561 (m-30) cc_final: 0.8132 (m-30) REVERT: L 50 ASP cc_start: 0.9221 (p0) cc_final: 0.9019 (p0) REVERT: I 105 GLN cc_start: 0.8850 (mp10) cc_final: 0.8602 (mp10) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2544 time to fit residues: 36.7089 Evaluate side-chains 79 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 111 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.027705 restraints weight = 96636.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.028758 restraints weight = 53223.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.029494 restraints weight = 35648.657| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12987 Z= 0.139 Angle : 0.518 8.616 17649 Z= 0.252 Chirality : 0.042 0.205 2034 Planarity : 0.004 0.050 2220 Dihedral : 5.460 41.786 2166 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.46 (0.22), residues: 1557 helix: 0.66 (0.39), residues: 204 sheet: -1.23 (0.23), residues: 444 loop : -1.20 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.009 0.001 HIS E 516 PHE 0.009 0.001 PHE A 234 TYR 0.007 0.001 TYR J 91 ARG 0.007 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.34 seconds wall clock time: 45 minutes 7.80 seconds (2707.80 seconds total)