Starting phenix.real_space_refine on Thu Feb 15 15:37:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/02_2024/6dzl_8935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/02_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_8935/02_2024/6dzl_8935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/02_2024/6dzl_8935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/02_2024/6dzl_8935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzl_8935/02_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 18 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: 18 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: 18 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: 6.79, per 1000 atoms: 0.53 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: 5.70 Conformation dependent library (CDL) restraints added in 2.3 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: 1.49 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: 3.67 Time building geometry restraints manager: 6.07 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: 7770 22.65 - 45.29: 192 45.29 - 67.94: 6 67.94 - 90.58: 18 90.58 - 113.23: 12 Dihedral angle restraints: 7998 sinusoidal: 3462 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 7995 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: 2.420 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: 14.950 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 37.310 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.960 ------------------------------------------------------------------------------- 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 : 11.385 113.229 5067 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 : 1.469 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: 0.3414 time to fit residues: 108.5608 Evaluate side-chains 94 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 ** 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12987 Z= 0.202 Angle : 0.643 7.644 17649 Z= 0.326 Chirality : 0.046 0.305 2034 Planarity : 0.005 0.040 2220 Dihedral : 9.840 74.327 2337 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -3.29 (0.20), residues: 1557 helix: -0.91 (0.36), residues: 198 sheet: -2.61 (0.21), residues: 408 loop : -2.33 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 518 HIS 0.003 0.001 HIS E 549 PHE 0.016 0.001 PHE D 572 TYR 0.013 0.002 TYR J 91 ARG 0.003 0.001 ARG H 83 *********************** 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 154 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.462 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: A 84 LYS cc_start: 0.9761 (mttt) cc_final: 0.9528 (mttp) REVERT: A 218 ILE cc_start: 0.8374 (mt) cc_final: 0.8165 (mp) REVERT: J 33 LEU cc_start: 0.8630 (tp) cc_final: 0.8427 (tp) REVERT: G 39 GLN cc_start: 0.9590 (tt0) cc_final: 0.9040 (tt0) REVERT: B 69 ASN cc_start: 0.8972 (m-40) cc_final: 0.8630 (m110) REVERT: B 84 LYS cc_start: 0.9787 (mttt) cc_final: 0.9562 (mttp) REVERT: H 39 GLN cc_start: 0.9612 (tt0) cc_final: 0.9294 (tt0) REVERT: H 73 ASN cc_start: 0.9339 (p0) cc_final: 0.8761 (m-40) REVERT: H 75 LYS cc_start: 0.9627 (ttmm) cc_final: 0.9383 (ttmm) REVERT: C 69 ASN cc_start: 0.8905 (m-40) cc_final: 0.8509 (m110) REVERT: C 84 LYS cc_start: 0.9747 (mttt) cc_final: 0.9536 (mttp) REVERT: L 74 THR cc_start: 0.9446 (t) cc_final: 0.9131 (t) REVERT: I 39 GLN cc_start: 0.9530 (tt0) cc_final: 0.9074 (tt0) REVERT: I 105 GLN cc_start: 0.8805 (mp10) cc_final: 0.8533 (mp10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2939 time to fit residues: 62.6078 Evaluate side-chains 99 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 69 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN J 37 GLN G 3 GLN G 6 GLN G 13 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** L 37 GLN I 6 GLN I 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12987 Z= 0.408 Angle : 0.730 6.927 17649 Z= 0.359 Chirality : 0.045 0.334 2034 Planarity : 0.005 0.045 2220 Dihedral : 9.505 71.092 2337 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -2.96 (0.20), residues: 1557 helix: -0.50 (0.37), residues: 198 sheet: -2.53 (0.21), residues: 459 loop : -2.00 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 104 HIS 0.017 0.002 HIS F 516 PHE 0.015 0.002 PHE C 132 TYR 0.015 0.002 TYR C 261 ARG 0.003 0.001 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 111 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.398 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: 0.9780 (mttt) cc_final: 0.9544 (mtmm) REVERT: A 127 ASP cc_start: 0.8831 (t70) cc_final: 0.8467 (t0) REVERT: A 140 LYS cc_start: 0.8991 (ptpp) cc_final: 0.8707 (ptpp) REVERT: A 218 ILE cc_start: 0.8579 (mt) cc_final: 0.8284 (mp) REVERT: D 552 ASP cc_start: 0.8662 (m-30) cc_final: 0.8070 (m-30) REVERT: J 33 LEU cc_start: 0.8708 (tp) cc_final: 0.8501 (tp) REVERT: J 74 THR cc_start: 0.9520 (t) cc_final: 0.9102 (t) REVERT: G 39 GLN cc_start: 0.9606 (tt0) cc_final: 0.9071 (tt0) REVERT: G 82 MET cc_start: 0.9069 (mpp) cc_final: 0.8617 (mpp) REVERT: E 552 ASP cc_start: 0.8812 (m-30) cc_final: 0.8296 (m-30) REVERT: H 73 ASN cc_start: 0.9181 (p0) cc_final: 0.8720 (m-40) REVERT: H 75 LYS cc_start: 0.9589 (ttmm) cc_final: 0.9362 (ttmm) REVERT: H 82 MET cc_start: 0.9038 (mpp) cc_final: 0.8579 (mpp) REVERT: F 552 ASP cc_start: 0.8336 (m-30) cc_final: 0.8074 (m-30) REVERT: I 82 MET cc_start: 0.9066 (mpp) cc_final: 0.8684 (mpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2888 time to fit residues: 45.0228 Evaluate side-chains 80 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 0.6980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** J 37 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12987 Z= 0.171 Angle : 0.563 9.064 17649 Z= 0.282 Chirality : 0.044 0.281 2034 Planarity : 0.004 0.052 2220 Dihedral : 8.605 62.815 2337 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.64 % Favored : 92.16 % 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: -2.38 (0.21), residues: 1557 helix: -0.07 (0.38), residues: 201 sheet: -2.10 (0.23), residues: 393 loop : -1.72 (0.21), residues: 963 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 0.015 0.001 PHE J 83 TYR 0.011 0.001 TYR C 261 ARG 0.002 0.000 ARG L 18 *********************** 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 118 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.300 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 84 LYS cc_start: 0.9762 (mttt) cc_final: 0.9520 (mtmm) REVERT: A 127 ASP cc_start: 0.8837 (t70) cc_final: 0.8460 (t0) REVERT: A 218 ILE cc_start: 0.8573 (mt) cc_final: 0.8327 (mp) REVERT: D 552 ASP cc_start: 0.8487 (m-30) cc_final: 0.7955 (m-30) REVERT: J 33 LEU cc_start: 0.8793 (tp) cc_final: 0.8494 (tp) REVERT: G 39 GLN cc_start: 0.9609 (tt0) cc_final: 0.9034 (tt0) REVERT: B 69 ASN cc_start: 0.9004 (m-40) cc_final: 0.8672 (m110) REVERT: B 84 LYS cc_start: 0.9768 (mttt) cc_final: 0.9542 (mtmm) REVERT: B 140 LYS cc_start: 0.9525 (ttpt) cc_final: 0.9256 (tppt) REVERT: E 552 ASP cc_start: 0.8599 (m-30) cc_final: 0.8084 (m-30) REVERT: E 569 LEU cc_start: 0.9840 (tp) cc_final: 0.9636 (tt) REVERT: K 74 THR cc_start: 0.9462 (t) cc_final: 0.9032 (t) REVERT: H 34 MET cc_start: 0.9432 (mmp) cc_final: 0.9194 (mmm) REVERT: H 73 ASN cc_start: 0.9148 (p0) cc_final: 0.8728 (m-40) REVERT: H 75 LYS cc_start: 0.9588 (ttmm) cc_final: 0.9336 (ttmm) REVERT: C 69 ASN cc_start: 0.8868 (m-40) cc_final: 0.8476 (m110) REVERT: C 84 LYS cc_start: 0.9772 (mttt) cc_final: 0.9559 (mtmm) REVERT: F 552 ASP cc_start: 0.8496 (m-30) cc_final: 0.7731 (m-30) REVERT: L 83 PHE cc_start: 0.8690 (m-80) cc_final: 0.8407 (m-80) REVERT: I 105 GLN cc_start: 0.8778 (mp10) cc_final: 0.8506 (mp10) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2883 time to fit residues: 47.5186 Evaluate side-chains 86 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 0.0050 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- 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** J 37 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12987 Z= 0.425 Angle : 0.729 6.801 17649 Z= 0.354 Chirality : 0.046 0.322 2034 Planarity : 0.004 0.054 2220 Dihedral : 8.625 60.313 2337 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % 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: -2.55 (0.21), residues: 1557 helix: -0.04 (0.38), residues: 201 sheet: -2.25 (0.21), residues: 501 loop : -1.71 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 99 HIS 0.012 0.001 HIS F 516 PHE 0.019 0.002 PHE B 132 TYR 0.016 0.002 TYR H 90 ARG 0.005 0.000 ARG J 18 *********************** 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 95 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.565 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: 0.9769 (mttt) cc_final: 0.9546 (mtmm) REVERT: A 127 ASP cc_start: 0.8862 (t70) cc_final: 0.8503 (t0) REVERT: D 552 ASP cc_start: 0.8678 (m-30) cc_final: 0.8169 (m-30) REVERT: J 33 LEU cc_start: 0.8857 (tp) cc_final: 0.8572 (tp) REVERT: G 82 MET cc_start: 0.9068 (mpp) cc_final: 0.8654 (mpp) REVERT: B 69 ASN cc_start: 0.9071 (m-40) cc_final: 0.8609 (m110) REVERT: B 140 LYS cc_start: 0.9524 (ttpt) cc_final: 0.9282 (tppt) REVERT: E 552 ASP cc_start: 0.8774 (m-30) cc_final: 0.8292 (m-30) REVERT: H 73 ASN cc_start: 0.9193 (p0) cc_final: 0.8691 (m-40) REVERT: H 75 LYS cc_start: 0.9537 (ttmm) cc_final: 0.9298 (ttmm) REVERT: C 69 ASN cc_start: 0.8995 (m-40) cc_final: 0.8465 (m110) REVERT: F 552 ASP cc_start: 0.8690 (m-30) cc_final: 0.7935 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2848 time to fit residues: 38.6785 Evaluate side-chains 68 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** J 37 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4342 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= 0.172 Angle : 0.569 9.452 17649 Z= 0.282 Chirality : 0.044 0.269 2034 Planarity : 0.004 0.053 2220 Dihedral : 7.946 53.519 2337 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % 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: -2.16 (0.22), residues: 1557 helix: 0.30 (0.38), residues: 204 sheet: -2.00 (0.22), residues: 444 loop : -1.53 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.007 0.001 HIS F 516 PHE 0.009 0.001 PHE F 582 TYR 0.010 0.001 TYR A 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 108 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.496 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: A 127 ASP cc_start: 0.8890 (t70) cc_final: 0.8562 (t0) REVERT: A 140 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8950 (ptpp) REVERT: A 218 ILE cc_start: 0.8680 (mt) cc_final: 0.8375 (mp) REVERT: D 552 ASP cc_start: 0.8510 (m-30) cc_final: 0.8089 (m-30) REVERT: J 33 LEU cc_start: 0.8871 (tp) cc_final: 0.8581 (tp) REVERT: B 44 GLN cc_start: 0.7654 (mp10) cc_final: 0.7452 (mp10) REVERT: B 69 ASN cc_start: 0.9020 (m-40) cc_final: 0.8689 (m110) REVERT: B 140 LYS cc_start: 0.9521 (ttpt) cc_final: 0.9257 (tppt) REVERT: B 260 ILE cc_start: 0.8619 (mm) cc_final: 0.8336 (tp) REVERT: E 552 ASP cc_start: 0.8744 (m-30) cc_final: 0.8255 (m-30) REVERT: K 75 ILE cc_start: 0.9128 (mp) cc_final: 0.8768 (tt) REVERT: H 34 MET cc_start: 0.9466 (mmp) cc_final: 0.9174 (mmm) REVERT: H 73 ASN cc_start: 0.9157 (p0) cc_final: 0.8663 (m-40) REVERT: H 75 LYS cc_start: 0.9544 (ttmm) cc_final: 0.9294 (ttmm) REVERT: C 69 ASN cc_start: 0.8988 (m-40) cc_final: 0.8642 (m110) REVERT: C 260 ILE cc_start: 0.8543 (mm) cc_final: 0.8258 (tp) REVERT: F 552 ASP cc_start: 0.8547 (m-30) cc_final: 0.7804 (m-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3233 time to fit residues: 48.0903 Evaluate side-chains 74 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 0.0370 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- 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** J 37 GLN 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12987 Z= 0.207 Angle : 0.568 7.325 17649 Z= 0.279 Chirality : 0.044 0.266 2034 Planarity : 0.004 0.050 2220 Dihedral : 7.567 49.370 2337 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -2.03 (0.22), residues: 1557 helix: 0.51 (0.38), residues: 204 sheet: -1.99 (0.21), residues: 468 loop : -1.39 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 531 HIS 0.007 0.001 HIS F 516 PHE 0.008 0.001 PHE B 132 TYR 0.011 0.001 TYR C 261 ARG 0.012 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 99 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.473 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 127 ASP cc_start: 0.8905 (t70) cc_final: 0.8576 (t0) REVERT: A 140 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8983 (ptpp) REVERT: A 218 ILE cc_start: 0.8699 (mt) cc_final: 0.8407 (mp) REVERT: D 552 ASP cc_start: 0.8603 (m-30) cc_final: 0.8102 (m-30) REVERT: J 33 LEU cc_start: 0.8873 (tp) cc_final: 0.8603 (tp) REVERT: B 69 ASN cc_start: 0.9086 (m-40) cc_final: 0.8778 (m110) REVERT: B 140 LYS cc_start: 0.9522 (ttpt) cc_final: 0.9238 (tppt) REVERT: B 260 ILE cc_start: 0.8635 (mm) cc_final: 0.8374 (tp) REVERT: E 552 ASP cc_start: 0.8730 (m-30) cc_final: 0.8234 (m-30) REVERT: K 55 GLU cc_start: 0.8707 (tp30) cc_final: 0.8441 (tp30) REVERT: H 34 MET cc_start: 0.9470 (mmp) cc_final: 0.9185 (mmm) REVERT: H 73 ASN cc_start: 0.9177 (p0) cc_final: 0.8669 (m-40) REVERT: H 75 LYS cc_start: 0.9538 (ttmm) cc_final: 0.9290 (ttmm) REVERT: C 69 ASN cc_start: 0.9078 (m-40) cc_final: 0.8696 (m110) REVERT: C 260 ILE cc_start: 0.8499 (mm) cc_final: 0.8238 (tp) REVERT: F 552 ASP cc_start: 0.8560 (m-30) cc_final: 0.7830 (m-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2854 time to fit residues: 40.3090 Evaluate side-chains 75 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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: 2.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** J 37 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** F 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12987 Z= 0.199 Angle : 0.552 7.834 17649 Z= 0.271 Chirality : 0.044 0.248 2034 Planarity : 0.004 0.050 2220 Dihedral : 7.192 54.897 2337 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % 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: -1.90 (0.21), residues: 1557 helix: 0.65 (0.38), residues: 204 sheet: -1.78 (0.21), residues: 486 loop : -1.38 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.008 0.001 HIS F 516 PHE 0.012 0.001 PHE K 62 TYR 0.010 0.001 TYR B 261 ARG 0.006 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 101 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.481 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 127 ASP cc_start: 0.8886 (t70) cc_final: 0.8564 (t0) REVERT: A 140 LYS cc_start: 0.9211 (ptpp) cc_final: 0.8949 (ptpp) REVERT: A 218 ILE cc_start: 0.8836 (mt) cc_final: 0.8577 (mp) REVERT: D 552 ASP cc_start: 0.8571 (m-30) cc_final: 0.8081 (m-30) REVERT: J 33 LEU cc_start: 0.8957 (tp) cc_final: 0.8715 (tp) REVERT: G 34 MET cc_start: 0.9494 (mmp) cc_final: 0.9282 (mmm) REVERT: B 69 ASN cc_start: 0.9062 (m-40) cc_final: 0.8668 (m110) REVERT: B 140 LYS cc_start: 0.9526 (ttpt) cc_final: 0.9250 (tptt) REVERT: B 260 ILE cc_start: 0.8636 (mm) cc_final: 0.8376 (tp) REVERT: E 552 ASP cc_start: 0.8705 (m-30) cc_final: 0.8183 (m-30) REVERT: H 34 MET cc_start: 0.9482 (mmp) cc_final: 0.9121 (mmm) REVERT: H 73 ASN cc_start: 0.9211 (p0) cc_final: 0.8719 (m-40) REVERT: H 75 LYS cc_start: 0.9509 (ttmm) cc_final: 0.9249 (ttmm) REVERT: C 69 ASN cc_start: 0.9009 (m-40) cc_final: 0.8540 (m110) REVERT: C 260 ILE cc_start: 0.8518 (mm) cc_final: 0.8285 (tp) REVERT: F 552 ASP cc_start: 0.8520 (m-30) cc_final: 0.8021 (m-30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2792 time to fit residues: 40.5492 Evaluate side-chains 74 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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: 7.9990 chunk 141 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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** J 37 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12987 Z= 0.180 Angle : 0.543 8.171 17649 Z= 0.268 Chirality : 0.043 0.235 2034 Planarity : 0.004 0.048 2220 Dihedral : 6.920 58.890 2337 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -1.75 (0.22), residues: 1557 helix: 0.77 (0.39), residues: 204 sheet: -1.69 (0.22), residues: 474 loop : -1.29 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 531 HIS 0.006 0.001 HIS F 516 PHE 0.008 0.001 PHE B 234 TYR 0.012 0.001 TYR K 87 ARG 0.005 0.000 ARG K 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 96 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.541 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 127 ASP cc_start: 0.8909 (t70) cc_final: 0.8594 (t0) REVERT: A 140 LYS cc_start: 0.9212 (ptpp) cc_final: 0.8945 (ptpp) REVERT: A 218 ILE cc_start: 0.8833 (mt) cc_final: 0.8567 (mp) REVERT: D 552 ASP cc_start: 0.8599 (m-30) cc_final: 0.8089 (m-30) REVERT: D 555 ILE cc_start: 0.9515 (mp) cc_final: 0.8894 (tt) REVERT: J 33 LEU cc_start: 0.8944 (tp) cc_final: 0.8699 (tp) REVERT: G 34 MET cc_start: 0.9493 (mmp) cc_final: 0.9177 (mmp) REVERT: B 69 ASN cc_start: 0.9070 (m-40) cc_final: 0.8685 (m110) REVERT: B 140 LYS cc_start: 0.9515 (ttpt) cc_final: 0.9267 (tppt) REVERT: B 260 ILE cc_start: 0.8617 (mm) cc_final: 0.8385 (tp) REVERT: E 552 ASP cc_start: 0.8719 (m-30) cc_final: 0.8201 (m-30) REVERT: H 34 MET cc_start: 0.9490 (mmp) cc_final: 0.8997 (mmm) REVERT: H 73 ASN cc_start: 0.9165 (p0) cc_final: 0.8732 (m-40) REVERT: C 69 ASN cc_start: 0.9060 (m-40) cc_final: 0.8568 (m110) REVERT: C 260 ILE cc_start: 0.8629 (mm) cc_final: 0.8375 (tp) REVERT: F 552 ASP cc_start: 0.8538 (m-30) cc_final: 0.8094 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2941 time to fit residues: 41.1409 Evaluate side-chains 75 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 0.1980 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 121 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 D 570 GLN J 37 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS ** 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** F 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12987 Z= 0.127 Angle : 0.525 8.751 17649 Z= 0.256 Chirality : 0.043 0.205 2034 Planarity : 0.004 0.049 2220 Dihedral : 6.445 59.428 2337 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -1.58 (0.21), residues: 1557 helix: 0.82 (0.39), residues: 204 sheet: -1.42 (0.22), residues: 465 loop : -1.26 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.005 0.001 HIS F 516 PHE 0.011 0.001 PHE B 234 TYR 0.008 0.001 TYR H 91 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 105 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.526 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: A 127 ASP cc_start: 0.8894 (t70) cc_final: 0.8583 (t0) REVERT: A 140 LYS cc_start: 0.9213 (ptpp) cc_final: 0.8948 (ptpp) REVERT: A 218 ILE cc_start: 0.8812 (mt) cc_final: 0.8548 (mp) REVERT: D 552 ASP cc_start: 0.8576 (m-30) cc_final: 0.8054 (m-30) REVERT: J 33 LEU cc_start: 0.8909 (tp) cc_final: 0.8676 (tp) REVERT: G 34 MET cc_start: 0.9546 (mmp) cc_final: 0.9325 (mmm) REVERT: B 69 ASN cc_start: 0.9032 (m-40) cc_final: 0.8771 (m110) REVERT: B 260 ILE cc_start: 0.8661 (mm) cc_final: 0.8428 (tp) REVERT: E 552 ASP cc_start: 0.8679 (m-30) cc_final: 0.8159 (m-30) REVERT: K 50 ASP cc_start: 0.9152 (p0) cc_final: 0.8947 (p0) REVERT: H 73 ASN cc_start: 0.9193 (p0) cc_final: 0.8733 (m-40) REVERT: C 69 ASN cc_start: 0.9029 (m-40) cc_final: 0.8655 (m110) REVERT: C 260 ILE cc_start: 0.8563 (mm) cc_final: 0.8342 (tp) REVERT: F 552 ASP cc_start: 0.8481 (m-30) cc_final: 0.8019 (m-30) REVERT: I 75 LYS cc_start: 0.9532 (ttmm) cc_final: 0.9305 (ttmm) REVERT: I 83 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8460 (mtm180) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2630 time to fit residues: 40.1693 Evaluate side-chains 79 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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** J 37 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.027580 restraints weight = 97094.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.028635 restraints weight = 53256.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.029398 restraints weight = 35727.348| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12987 Z= 0.153 Angle : 0.533 8.524 17649 Z= 0.261 Chirality : 0.042 0.206 2034 Planarity : 0.004 0.047 2220 Dihedral : 6.226 58.360 2337 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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: -1.48 (0.22), residues: 1557 helix: 0.75 (0.38), residues: 204 sheet: -1.35 (0.22), residues: 522 loop : -1.10 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 104 HIS 0.022 0.002 HIS D 516 PHE 0.010 0.001 PHE B 234 TYR 0.010 0.001 TYR K 87 ARG 0.006 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2342.81 seconds wall clock time: 44 minutes 26.78 seconds (2666.78 seconds total)