Starting phenix.real_space_refine on Sun Feb 18 08:57:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/02_2024/6zbb_11149_trim_updated.pdb" } resolution = 3.61 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= 0.001 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 55 5.16 5 C 6974 2.51 5 N 1617 2.21 5 O 1836 1.98 5 H 10446 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 GLU 38": "OE1" <-> "OE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 58": "OE1" <-> "OE2" Residue "P PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 3": "OD1" <-> "OD2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "a PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 137": "OE1" <-> "OE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ASP 51": "OD1" <-> "OD2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e ARG 58": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 13": "OE1" <-> "OE2" Residue "f ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ASP 42": "OD1" <-> "OD2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 20936 Number of models: 1 Model: "" Number of chains: 20 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3557 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "b" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1791 Classifications: {'peptide': 112} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "d" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 893 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 45} Chain: "e" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 975 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 161 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "f" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 9.48, per 1000 atoms: 0.45 Number of scatterers: 20936 At special positions: 0 Unit cell: (110.04, 125.76, 121.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 8 15.00 O 1836 8.00 N 1617 7.00 C 6974 6.00 H 10446 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.63 Conformation dependent library (CDL) restraints added in 2.1 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 20 removed outlier: 4.532A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU 8 14 " --> pdb=" O THR 8 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER 8 15 " --> pdb=" O MET 8 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 30 removed outlier: 3.568A pdb=" N SER 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 38 removed outlier: 4.043A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 3.934A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 38 removed outlier: 4.355A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 72 removed outlier: 3.892A pdb=" N LEU L 52 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 37 removed outlier: 5.097A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 4.271A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 37 removed outlier: 4.148A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.833A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 38 removed outlier: 3.782A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.268A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 38 removed outlier: 4.539A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 72 removed outlier: 3.737A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 4.359A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.619A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 38 removed outlier: 3.902A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 72 removed outlier: 3.762A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 9 No H-bonds generated for 'chain 'a' and resid 7 through 9' Processing helix chain 'a' and resid 19 through 30 removed outlier: 4.268A pdb=" N VAL a 24 " --> pdb=" O THR a 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 57 removed outlier: 4.072A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 86 removed outlier: 5.305A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 128 Proline residue: a 107 - end of helix removed outlier: 7.486A pdb=" N LYS a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA a 123 " --> pdb=" O ASN a 119 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 150 Proline residue: a 139 - end of helix removed outlier: 4.891A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 183 removed outlier: 3.656A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS a 172 " --> pdb=" O HIS a 168 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 225 removed outlier: 3.787A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'b' and resid 19 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 47 Processing helix chain 'b' and resid 55 through 111 removed outlier: 5.905A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 122 removed outlier: 3.677A pdb=" N LYS d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 removed outlier: 3.877A pdb=" N GLU d 137 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'd' and resid 146 through 148 No H-bonds generated for 'chain 'd' and resid 146 through 148' Processing helix chain 'e' and resid 8 through 56 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 17 through 25 Proline residue: f 20 - end of helix Processing helix chain 'f' and resid 30 through 48 removed outlier: 3.856A pdb=" N ALA f 36 " --> pdb=" O GLY f 32 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 74 removed outlier: 3.654A pdb=" N SER f 60 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU f 63 " --> pdb=" O SER f 60 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL f 67 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU f 69 " --> pdb=" O TYR f 66 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG f 73 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 81 No H-bonds generated for 'chain 'f' and resid 79 through 81' Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.701A pdb=" N ALA g 27 " --> pdb=" O LYS g 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 61 Proline residue: g 46 - end of helix removed outlier: 3.571A pdb=" N LYS g 60 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 66 Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.568A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 18 removed outlier: 4.364A pdb=" N ILE j 11 " --> pdb=" O LYS j 7 " (cutoff:3.500A) Proline residue: j 12 - end of helix Proline residue: j 15 - end of helix Processing helix chain 'j' and resid 24 through 47 Processing helix chain 'k' and resid 14 through 17 No H-bonds generated for 'chain 'k' and resid 14 through 17' Processing helix chain 'k' and resid 24 through 45 741 hydrogen bonds defined for protein. 2082 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: 7.88 Time building geometry restraints manager: 19.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10436 1.03 - 1.23: 121 1.23 - 1.43: 4165 1.43 - 1.62: 6307 1.62 - 1.82: 114 Bond restraints: 21143 Sorted by residual: bond pdb=" CB7 CDL a 301 " pdb=" OB8 CDL a 301 " ideal model delta sigma weight residual 1.334 1.406 -0.072 1.10e-02 8.26e+03 4.25e+01 bond pdb=" CB7 CDL b 301 " pdb=" OB8 CDL b 301 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" CB7 CDL b 302 " pdb=" OB8 CDL b 302 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.03e+01 bond pdb=" CA7 CDL b 302 " pdb=" OA8 CDL b 302 " ideal model delta sigma weight residual 1.334 1.398 -0.064 1.10e-02 8.26e+03 3.38e+01 bond pdb=" CA7 CDL a 301 " pdb=" OA8 CDL a 301 " ideal model delta sigma weight residual 1.334 1.397 -0.063 1.10e-02 8.26e+03 3.26e+01 ... (remaining 21138 not shown) Histogram of bond angle deviations from ideal: 95.06 - 102.85: 66 102.85 - 110.64: 22416 110.64 - 118.43: 6398 118.43 - 126.21: 9059 126.21 - 134.00: 141 Bond angle restraints: 38080 Sorted by residual: angle pdb=" C51 CDL b 302 " pdb=" CB5 CDL b 302 " pdb=" OB6 CDL b 302 " ideal model delta sigma weight residual 111.33 121.07 -9.74 1.32e+00 5.72e-01 5.43e+01 angle pdb=" C11 CDL b 302 " pdb=" CA5 CDL b 302 " pdb=" OA6 CDL b 302 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C11 CDL a 301 " pdb=" CA5 CDL a 301 " pdb=" OA6 CDL a 301 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C11 CDL b 301 " pdb=" CA5 CDL b 301 " pdb=" OA6 CDL b 301 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 angle pdb=" C51 CDL a 301 " pdb=" CB5 CDL a 301 " pdb=" OB6 CDL a 301 " ideal model delta sigma weight residual 111.33 119.88 -8.55 1.32e+00 5.72e-01 4.18e+01 ... (remaining 38075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 8879 20.26 - 40.52: 763 40.52 - 60.79: 403 60.79 - 81.05: 14 81.05 - 101.31: 8 Dihedral angle restraints: 10067 sinusoidal: 5529 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LEU M 62 " pdb=" C LEU M 62 " pdb=" N PHE M 63 " pdb=" CA PHE M 63 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS b 48 " pdb=" C LYS b 48 " pdb=" N GLU b 49 " pdb=" CA GLU b 49 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE M 29 " pdb=" C PHE M 29 " pdb=" N GLY M 30 " pdb=" CA GLY M 30 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1068 0.034 - 0.069: 424 0.069 - 0.103: 111 0.103 - 0.137: 39 0.137 - 0.172: 9 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE R 9 " pdb=" CA ILE R 9 " pdb=" CG1 ILE R 9 " pdb=" CG2 ILE R 9 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PRO a 89 " pdb=" N PRO a 89 " pdb=" C PRO a 89 " pdb=" CB PRO a 89 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU M 62 " pdb=" N LEU M 62 " pdb=" C LEU M 62 " pdb=" CB LEU M 62 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1648 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 101 " -0.067 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C8 LHG f 101 " 0.020 2.00e-02 2.50e+03 pdb=" O7 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O9 LHG f 101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 101 " -0.057 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C24 LHG f 101 " 0.017 2.00e-02 2.50e+03 pdb=" O10 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O8 LHG f 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 102 " 0.054 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C8 LHG f 102 " -0.016 2.00e-02 2.50e+03 pdb=" O7 LHG f 102 " -0.017 2.00e-02 2.50e+03 pdb=" O9 LHG f 102 " -0.022 2.00e-02 2.50e+03 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 467 2.08 - 2.71: 35942 2.71 - 3.34: 64003 3.34 - 3.97: 75675 3.97 - 4.60: 121689 Nonbonded interactions: 297776 Sorted by model distance: nonbonded pdb="HH22 ARG a 36 " pdb=" O PRO b 3 " model vdw 1.453 1.850 nonbonded pdb=" O GLY k 13 " pdb=" H TYR k 17 " model vdw 1.490 1.850 nonbonded pdb=" O ILE R 2 " pdb=" H ALA R 6 " model vdw 1.491 1.850 nonbonded pdb=" OD1 ASN 8 32 " pdb=" H PHE 8 33 " model vdw 1.527 1.850 nonbonded pdb=" H THR d 131 " pdb=" OD2 ASP d 134 " model vdw 1.528 1.850 ... (remaining 297771 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 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } 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: 6.930 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: 0.320 Extract box with map and model: 26.850 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 67.580 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.008 0.083 10697 Z= 0.483 Angle : 1.035 12.413 14408 Z= 0.515 Chirality : 0.042 0.172 1651 Planarity : 0.004 0.041 1726 Dihedral : 17.259 101.309 3971 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1270 helix: 0.37 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 85 HIS 0.013 0.002 HIS b 8 PHE 0.036 0.002 PHE M 47 TYR 0.013 0.001 TYR N 49 ARG 0.014 0.001 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.501 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: K 3 ASP cc_start: 0.8110 (m-30) cc_final: 0.7759 (m-30) REVERT: a 203 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8302 (mm-30) REVERT: b 102 LYS cc_start: 0.9146 (tttt) cc_final: 0.8913 (tttt) REVERT: d 158 GLU cc_start: 0.8497 (pm20) cc_final: 0.8161 (pm20) REVERT: g 82 VAL cc_start: 0.9061 (m) cc_final: 0.8842 (p) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.4367 time to fit residues: 160.5793 Evaluate side-chains 205 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10697 Z= 0.299 Angle : 0.632 7.214 14408 Z= 0.335 Chirality : 0.039 0.154 1651 Planarity : 0.004 0.057 1726 Dihedral : 14.442 109.382 1740 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.53 % Allowed : 8.92 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1270 helix: 0.37 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 109 HIS 0.008 0.001 HIS b 8 PHE 0.026 0.002 PHE M 47 TYR 0.011 0.001 TYR k 43 ARG 0.005 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.614 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: K 3 ASP cc_start: 0.8112 (m-30) cc_final: 0.7737 (m-30) REVERT: K 54 PHE cc_start: 0.8191 (t80) cc_final: 0.7940 (t80) REVERT: P 63 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6384 (p90) REVERT: j 7 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7986 (mmmt) outliers start: 16 outliers final: 14 residues processed: 229 average time/residue: 0.4445 time to fit residues: 151.3009 Evaluate side-chains 216 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 55 ILE Chi-restraints excluded: chain g residue 84 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10697 Z= 0.267 Angle : 0.598 6.139 14408 Z= 0.315 Chirality : 0.038 0.149 1651 Planarity : 0.004 0.062 1726 Dihedral : 13.478 106.847 1740 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.82 % Allowed : 11.41 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1270 helix: 0.49 (0.16), residues: 1016 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 85 HIS 0.005 0.001 HIS b 8 PHE 0.021 0.001 PHE M 47 TYR 0.009 0.001 TYR f 71 ARG 0.005 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 1.796 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: K 3 ASP cc_start: 0.8101 (m-30) cc_final: 0.7726 (m-30) REVERT: K 54 PHE cc_start: 0.8155 (t80) cc_final: 0.7923 (t80) REVERT: g 66 GLN cc_start: 0.8464 (mm110) cc_final: 0.8065 (pp30) outliers start: 19 outliers final: 14 residues processed: 230 average time/residue: 0.4540 time to fit residues: 155.1440 Evaluate side-chains 217 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10697 Z= 0.221 Angle : 0.572 7.085 14408 Z= 0.299 Chirality : 0.037 0.141 1651 Planarity : 0.004 0.059 1726 Dihedral : 12.709 105.714 1740 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.73 % Allowed : 12.75 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1270 helix: 0.61 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -1.29 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 PHE 0.019 0.001 PHE K 63 TYR 0.009 0.001 TYR f 71 ARG 0.004 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.796 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: K 3 ASP cc_start: 0.8071 (m-30) cc_final: 0.7728 (m-30) REVERT: R 38 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8199 (ttm-80) REVERT: g 66 GLN cc_start: 0.8405 (mm110) cc_final: 0.8031 (pp30) outliers start: 18 outliers final: 15 residues processed: 233 average time/residue: 0.4394 time to fit residues: 150.0717 Evaluate side-chains 227 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10697 Z= 0.201 Angle : 0.565 7.700 14408 Z= 0.294 Chirality : 0.037 0.179 1651 Planarity : 0.004 0.058 1726 Dihedral : 11.853 104.837 1740 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.30 % Allowed : 13.04 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1270 helix: 0.76 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.20 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.024 0.001 PHE K 63 TYR 0.009 0.001 TYR e 15 ARG 0.004 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.770 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: K 3 ASP cc_start: 0.8056 (m-30) cc_final: 0.7707 (m-30) REVERT: M 62 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7199 (mp) REVERT: N 75 MET cc_start: 0.5350 (mmm) cc_final: 0.5096 (mmm) REVERT: d 158 GLU cc_start: 0.8403 (pm20) cc_final: 0.8191 (pm20) REVERT: g 66 GLN cc_start: 0.8375 (mm110) cc_final: 0.8028 (pp30) REVERT: j 31 MET cc_start: 0.8790 (tmm) cc_final: 0.8394 (tmm) outliers start: 24 outliers final: 17 residues processed: 241 average time/residue: 0.4327 time to fit residues: 153.2960 Evaluate side-chains 234 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10697 Z= 0.250 Angle : 0.573 8.053 14408 Z= 0.300 Chirality : 0.037 0.154 1651 Planarity : 0.004 0.031 1726 Dihedral : 11.609 105.337 1740 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.59 % Allowed : 12.66 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1270 helix: 0.78 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.22 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.009 0.001 TYR e 15 ARG 0.004 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 1.634 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: K 3 ASP cc_start: 0.8076 (m-30) cc_final: 0.7715 (m-30) REVERT: M 62 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7276 (mp) REVERT: d 158 GLU cc_start: 0.8407 (pm20) cc_final: 0.8150 (pm20) REVERT: g 66 GLN cc_start: 0.8372 (mm110) cc_final: 0.8017 (pp30) REVERT: j 7 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7713 (mmmt) outliers start: 27 outliers final: 22 residues processed: 230 average time/residue: 0.4363 time to fit residues: 147.7244 Evaluate side-chains 230 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 101 optimal weight: 0.0170 chunk 67 optimal weight: 0.2980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10697 Z= 0.169 Angle : 0.546 8.047 14408 Z= 0.281 Chirality : 0.036 0.142 1651 Planarity : 0.003 0.034 1726 Dihedral : 11.008 103.091 1740 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.21 % Allowed : 13.61 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1270 helix: 0.98 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.028 0.001 PHE K 63 TYR 0.011 0.001 TYR e 15 ARG 0.003 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.655 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: 8 10 LEU cc_start: 0.8981 (tp) cc_final: 0.8777 (tp) REVERT: K 3 ASP cc_start: 0.8065 (m-30) cc_final: 0.7660 (m-30) REVERT: d 158 GLU cc_start: 0.8384 (pm20) cc_final: 0.8132 (pm20) REVERT: j 7 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7728 (mmmt) REVERT: j 31 MET cc_start: 0.8784 (tmm) cc_final: 0.8400 (tmm) outliers start: 23 outliers final: 17 residues processed: 233 average time/residue: 0.4313 time to fit residues: 149.3251 Evaluate side-chains 225 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10697 Z= 0.211 Angle : 0.562 8.192 14408 Z= 0.291 Chirality : 0.037 0.154 1651 Planarity : 0.003 0.037 1726 Dihedral : 10.797 103.970 1740 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.82 % Allowed : 14.57 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1270 helix: 1.00 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.90 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.027 0.001 PHE K 63 TYR 0.008 0.001 TYR e 15 ARG 0.003 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.567 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: 8 10 LEU cc_start: 0.9009 (tp) cc_final: 0.8805 (tp) REVERT: K 3 ASP cc_start: 0.8082 (m-30) cc_final: 0.7666 (m-30) REVERT: d 158 GLU cc_start: 0.8403 (pm20) cc_final: 0.8160 (pm20) REVERT: j 7 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7709 (mmmt) REVERT: j 31 MET cc_start: 0.8809 (tmm) cc_final: 0.8405 (tmm) outliers start: 19 outliers final: 16 residues processed: 223 average time/residue: 0.4495 time to fit residues: 148.1156 Evaluate side-chains 226 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10697 Z= 0.221 Angle : 0.566 8.059 14408 Z= 0.294 Chirality : 0.037 0.204 1651 Planarity : 0.003 0.040 1726 Dihedral : 10.670 103.781 1740 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.88 % Allowed : 13.81 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1270 helix: 1.02 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -0.88 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.007 0.001 TYR f 71 ARG 0.003 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.622 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: K 3 ASP cc_start: 0.8103 (m-30) cc_final: 0.7692 (m-30) REVERT: M 36 TYR cc_start: 0.7454 (t80) cc_final: 0.6923 (t80) REVERT: Q 47 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6427 (t80) REVERT: b 51 TYR cc_start: 0.8392 (t80) cc_final: 0.8165 (t80) REVERT: d 158 GLU cc_start: 0.8388 (pm20) cc_final: 0.8148 (pm20) REVERT: j 7 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7665 (mmmt) outliers start: 30 outliers final: 25 residues processed: 230 average time/residue: 0.4442 time to fit residues: 150.3929 Evaluate side-chains 238 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 100 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 105 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10697 Z= 0.173 Angle : 0.559 7.948 14408 Z= 0.287 Chirality : 0.037 0.208 1651 Planarity : 0.003 0.047 1726 Dihedral : 10.300 101.841 1740 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.49 % Allowed : 14.57 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.09 (0.25), residues: 1270 helix: 1.12 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -0.69 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 85 HIS 0.002 0.001 HIS b 8 PHE 0.027 0.001 PHE K 63 TYR 0.008 0.001 TYR e 15 ARG 0.002 0.000 ARG R 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 231 time to evaluate : 1.599 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: K 3 ASP cc_start: 0.8077 (m-30) cc_final: 0.7662 (m-30) REVERT: Q 47 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6394 (t80) REVERT: b 51 TYR cc_start: 0.8393 (t80) cc_final: 0.8182 (t80) REVERT: d 158 GLU cc_start: 0.8397 (pm20) cc_final: 0.8127 (pm20) REVERT: j 7 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7683 (ptpt) REVERT: k 14 ILE cc_start: 0.8723 (mm) cc_final: 0.8237 (mt) outliers start: 26 outliers final: 23 residues processed: 242 average time/residue: 0.4236 time to fit residues: 150.7473 Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 9 ILE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain e residue 18 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain k residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** d 129 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 = 0.3649 r_free = 0.3649 target = 0.105020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085201 restraints weight = 73488.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088197 restraints weight = 32168.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089917 restraints weight = 20083.007| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10697 Z= 0.230 Angle : 0.577 8.144 14408 Z= 0.302 Chirality : 0.037 0.200 1651 Planarity : 0.004 0.045 1726 Dihedral : 10.356 103.214 1740 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.21 % Allowed : 15.24 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.03 (0.25), residues: 1270 helix: 1.11 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.007 0.001 TYR L 49 ARG 0.004 0.000 ARG R 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4749.90 seconds wall clock time: 85 minutes 41.05 seconds (5141.05 seconds total)