Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 01:54:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zyd_11557/10_2023/6zyd_11557_trim_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.010 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 7 5.49 5 S 70 5.16 5 C 10927 2.51 5 N 2849 2.21 5 O 3080 1.98 5 H 14490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 260": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 260": "OE1" <-> "OE2" Residue "A ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 260": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 260": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 260": "OE1" <-> "OE2" Residue "F ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 260": "OE1" <-> "OE2" Residue "G ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 31423 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.03, per 1000 atoms: 0.41 Number of scatterers: 31423 At special positions: 0 Unit cell: (103.16, 104.223, 134.001, 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 70 16.00 P 7 15.00 O 3080 8.00 N 2849 7.00 C 10927 6.00 H 14490 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: 25.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 14 sheets defined 75.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'E' and resid -65 through -48 removed outlier: 3.679A pdb=" N UNK E -55 " --> pdb=" O UNK E -59 " (cutoff:3.500A) Processing helix chain 'E' and resid -38 through -34 Processing helix chain 'E' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK E -14 " --> pdb=" O UNK E -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK E -13 " --> pdb=" O UNK E -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK E -8 " --> pdb=" O UNK E -12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N UNK E -5 " --> pdb=" O UNK E -9 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 138 removed outlier: 3.638A pdb=" N VAL E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 175 removed outlier: 5.322A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY E 252 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL E 253 " --> pdb=" O LYS E 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 263 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 320 Processing helix chain 'C' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK C -55 " --> pdb=" O UNK C -59 " (cutoff:3.500A) Processing helix chain 'C' and resid -38 through -34 Processing helix chain 'C' and resid -32 through -5 removed outlier: 3.725A pdb=" N UNK C -14 " --> pdb=" O UNK C -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK C -13 " --> pdb=" O UNK C -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK C -8 " --> pdb=" O UNK C -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK C -5 " --> pdb=" O UNK C -9 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 175 removed outlier: 5.320A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 245 through 264 removed outlier: 3.566A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 253 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 263 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 320 Processing helix chain 'A' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK A -55 " --> pdb=" O UNK A -59 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -34 Processing helix chain 'A' and resid -32 through -5 removed outlier: 3.724A pdb=" N UNK A -14 " --> pdb=" O UNK A -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK A -13 " --> pdb=" O UNK A -17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK A -8 " --> pdb=" O UNK A -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK A -5 " --> pdb=" O UNK A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.848A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 138 removed outlier: 3.637A pdb=" N VAL A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 175 removed outlier: 5.321A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY A 252 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 253 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 320 Processing helix chain 'B' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK B -55 " --> pdb=" O UNK B -59 " (cutoff:3.500A) Processing helix chain 'B' and resid -38 through -34 Processing helix chain 'B' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK B -14 " --> pdb=" O UNK B -18 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N UNK B -13 " --> pdb=" O UNK B -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK B -8 " --> pdb=" O UNK B -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK B -5 " --> pdb=" O UNK B -9 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 138 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 175 removed outlier: 5.321A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 253 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 263 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 320 Processing helix chain 'D' and resid -65 through -48 removed outlier: 3.679A pdb=" N UNK D -55 " --> pdb=" O UNK D -59 " (cutoff:3.500A) Processing helix chain 'D' and resid -38 through -34 Processing helix chain 'D' and resid -32 through -5 removed outlier: 3.724A pdb=" N UNK D -14 " --> pdb=" O UNK D -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK D -13 " --> pdb=" O UNK D -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK D -8 " --> pdb=" O UNK D -12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N UNK D -5 " --> pdb=" O UNK D -9 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.851A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 175 removed outlier: 5.323A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY D 252 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 253 " --> pdb=" O LYS D 250 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS D 263 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 320 Processing helix chain 'F' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK F -55 " --> pdb=" O UNK F -59 " (cutoff:3.500A) Processing helix chain 'F' and resid -38 through -34 Processing helix chain 'F' and resid -32 through -5 removed outlier: 3.725A pdb=" N UNK F -14 " --> pdb=" O UNK F -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK F -13 " --> pdb=" O UNK F -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK F -8 " --> pdb=" O UNK F -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK F -5 " --> pdb=" O UNK F -9 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 138 removed outlier: 3.636A pdb=" N VAL F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 175 removed outlier: 5.322A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'F' and resid 229 through 231 No H-bonds generated for 'chain 'F' and resid 229 through 231' Processing helix chain 'F' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY F 252 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL F 253 " --> pdb=" O LYS F 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 263 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 320 Processing helix chain 'G' and resid -65 through -48 removed outlier: 3.680A pdb=" N UNK G -55 " --> pdb=" O UNK G -59 " (cutoff:3.500A) Processing helix chain 'G' and resid -38 through -34 Processing helix chain 'G' and resid -32 through -5 removed outlier: 3.726A pdb=" N UNK G -14 " --> pdb=" O UNK G -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK G -13 " --> pdb=" O UNK G -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK G -8 " --> pdb=" O UNK G -12 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N UNK G -5 " --> pdb=" O UNK G -9 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 109 removed outlier: 3.850A pdb=" N THR G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY G 109 " --> pdb=" O GLN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 138 removed outlier: 3.637A pdb=" N VAL G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 175 removed outlier: 5.323A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 245 through 264 removed outlier: 3.567A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY G 252 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL G 253 " --> pdb=" O LYS G 250 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 263 " --> pdb=" O GLU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 320 Processing sheet with id= A, first strand: chain 'E' and resid 213 through 217 removed outlier: 5.579A pdb=" N THR E 207 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL E 196 " --> pdb=" O THR E 207 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 213 through 217 removed outlier: 5.579A pdb=" N THR C 207 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 196 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 213 through 217 removed outlier: 5.580A pdb=" N THR A 207 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL A 196 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR B 207 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL B 196 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR D 207 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL D 196 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 213 through 217 removed outlier: 5.580A pdb=" N THR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL F 196 " --> pdb=" O THR F 207 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR F 291 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL F 276 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 213 through 217 removed outlier: 5.581A pdb=" N THR G 207 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL G 196 " --> pdb=" O THR G 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.603A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 2898 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: 11.39 Time building geometry restraints manager: 26.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14476 1.02 - 1.21: 21 1.21 - 1.41: 6972 1.41 - 1.61: 10087 1.61 - 1.81: 140 Bond restraints: 31696 Sorted by residual: bond pdb=" SG CYS C 292 " pdb=" HG CYS C 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" SG CYS A 292 " pdb=" HG CYS A 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS E 292 " pdb=" HG CYS E 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS G 292 " pdb=" HG CYS G 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" SG CYS B 292 " pdb=" HG CYS B 292 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 31691 not shown) Histogram of bond angle deviations from ideal: 78.71 - 89.75: 42 89.75 - 100.78: 56 100.78 - 111.81: 34124 111.81 - 122.84: 18478 122.84 - 133.87: 3356 Bond angle restraints: 56056 Sorted by residual: angle pdb=" CG2 THR A 113 " pdb=" CB THR A 113 " pdb=" HB THR A 113 " ideal model delta sigma weight residual 108.00 78.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR D 113 " pdb=" CB THR D 113 " pdb=" HB THR D 113 " ideal model delta sigma weight residual 108.00 78.72 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR E 113 " pdb=" CB THR E 113 " pdb=" HB THR E 113 " ideal model delta sigma weight residual 108.00 78.75 29.25 3.00e+00 1.11e-01 9.51e+01 angle pdb=" CG2 THR C 113 " pdb=" CB THR C 113 " pdb=" HB THR C 113 " ideal model delta sigma weight residual 108.00 78.76 29.24 3.00e+00 1.11e-01 9.50e+01 angle pdb=" CG2 THR B 113 " pdb=" CB THR B 113 " pdb=" HB THR B 113 " ideal model delta sigma weight residual 108.00 78.77 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 56051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 12971 35.28 - 70.56: 273 70.56 - 105.84: 21 105.84 - 141.12: 7 141.12 - 176.40: 14 Dihedral angle restraints: 13286 sinusoidal: 5698 harmonic: 7588 Sorted by residual: dihedral pdb=" CA ILE G 192 " pdb=" C ILE G 192 " pdb=" N GLU G 193 " pdb=" CA GLU G 193 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE C 192 " pdb=" C ILE C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE A 192 " pdb=" C ILE A 192 " pdb=" N GLU A 193 " pdb=" CA GLU A 193 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 13283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 2758 0.293 - 0.585: 0 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 14 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CB THR G 113 " pdb=" CA THR G 113 " pdb=" OG1 THR G 113 " pdb=" CG2 THR G 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR C 113 " pdb=" CA THR C 113 " pdb=" OG1 THR C 113 " pdb=" CG2 THR C 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.32e+01 chirality pdb=" CB THR F 113 " pdb=" CA THR F 113 " pdb=" OG1 THR F 113 " pdb=" CG2 THR F 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.31e+01 ... (remaining 2769 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 282 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" N ASP B 283 " 0.047 2.00e-02 2.50e+03 pdb=" CA ASP B 283 " -0.012 2.00e-02 2.50e+03 pdb=" H ASP B 283 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 282 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" N ASP F 283 " -0.047 2.00e-02 2.50e+03 pdb=" CA ASP F 283 " 0.012 2.00e-02 2.50e+03 pdb=" H ASP F 283 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 133 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" N TYR F 134 " -0.047 2.00e-02 2.50e+03 pdb=" CA TYR F 134 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR F 134 " 0.021 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 892 2.12 - 2.74: 55381 2.74 - 3.36: 82956 3.36 - 3.98: 108543 3.98 - 4.60: 172377 Nonbonded interactions: 420149 Sorted by model distance: nonbonded pdb="HD12 ILE E 268 " pdb=" HG CYS E 292 " model vdw 1.506 2.440 nonbonded pdb="HD12 ILE F 268 " pdb=" HG CYS F 292 " model vdw 1.528 2.440 nonbonded pdb=" HA3 GLY E 144 " pdb="HD23 LEU F 133 " model vdw 1.672 2.440 nonbonded pdb="HD23 LEU C 133 " pdb=" HA3 GLY G 144 " model vdw 1.678 2.440 nonbonded pdb="HD23 LEU E 133 " pdb=" HA3 GLY D 144 " model vdw 1.692 2.440 ... (remaining 420144 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic 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: 0.470 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: 0.520 Extract box with map and model: 3.450 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 95.600 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.170 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.017 0.107 17206 Z= 1.058 Angle : 1.196 16.094 23310 Z= 0.630 Chirality : 0.120 1.463 2772 Planarity : 0.007 0.067 2926 Dihedral : 17.406 176.400 5985 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.12 (0.17), residues: 1778 helix: -1.47 (0.13), residues: 938 sheet: -2.68 (0.28), residues: 259 loop : -2.47 (0.24), residues: 581 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.401 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 outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 2.2658 time to fit residues: 547.2499 Evaluate side-chains 125 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 272 GLN E 307 GLN E 329 GLN C 272 GLN C 307 GLN C 329 GLN A 99 ASN A 272 GLN A 307 GLN A 329 GLN B 272 GLN B 307 GLN B 329 GLN D 99 ASN D 272 GLN D 307 GLN D 329 GLN F 272 GLN F 307 GLN F 329 GLN G 99 ASN G 272 GLN G 307 GLN G 329 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.259 17206 Z= 3.172 Angle : 1.918 12.705 23310 Z= 1.069 Chirality : 0.168 1.463 2772 Planarity : 0.012 0.091 2926 Dihedral : 16.853 169.771 2653 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 40.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.62 % Favored : 90.27 % Rotamer: Outliers : 6.41 % Allowed : 16.91 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.30 (0.15), residues: 1778 helix: -2.57 (0.13), residues: 938 sheet: -2.60 (0.28), residues: 259 loop : -3.07 (0.20), residues: 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 175 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 58 residues processed: 255 average time/residue: 1.7946 time to fit residues: 533.8771 Evaluate side-chains 226 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 168 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 53 residues processed: 5 average time/residue: 1.8332 time to fit residues: 13.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.261 17206 Z= 3.187 Angle : 1.949 12.903 23310 Z= 1.081 Chirality : 0.169 1.509 2772 Planarity : 0.012 0.084 2926 Dihedral : 14.626 161.064 2653 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 47.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.89 % Favored : 86.00 % Rotamer: Outliers : 15.12 % Allowed : 16.59 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -5.35 (0.14), residues: 1778 helix: -3.35 (0.12), residues: 952 sheet: -2.78 (0.28), residues: 245 loop : -3.84 (0.17), residues: 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 157 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 236 outliers final: 121 residues processed: 357 average time/residue: 1.2527 time to fit residues: 549.2917 Evaluate side-chains 269 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 148 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 112 residues processed: 9 average time/residue: 0.7100 time to fit residues: 11.6912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.256 17206 Z= 3.171 Angle : 1.911 12.449 23310 Z= 1.062 Chirality : 0.167 1.513 2772 Planarity : 0.013 0.092 2926 Dihedral : 15.036 137.525 2653 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 51.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.10 % Favored : 82.90 % Rotamer: Outliers : 15.95 % Allowed : 17.94 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -5.77 (0.14), residues: 1778 helix: -3.65 (0.11), residues: 973 sheet: -3.05 (0.27), residues: 259 loop : -4.04 (0.18), residues: 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 144 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 249 outliers final: 158 residues processed: 356 average time/residue: 1.2294 time to fit residues: 544.2266 Evaluate side-chains 293 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 135 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 158 outliers final: 150 residues processed: 9 average time/residue: 1.0279 time to fit residues: 14.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.254 17206 Z= 3.171 Angle : 1.907 12.940 23310 Z= 1.060 Chirality : 0.168 1.536 2772 Planarity : 0.013 0.096 2926 Dihedral : 14.860 143.868 2653 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 52.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.62 % Favored : 81.38 % Rotamer: Outliers : 16.21 % Allowed : 18.96 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.93 (0.13), residues: 1778 helix: -3.71 (0.11), residues: 952 sheet: -3.11 (0.27), residues: 259 loop : -4.30 (0.16), residues: 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 141 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 160 residues processed: 361 average time/residue: 1.1849 time to fit residues: 530.1104 Evaluate side-chains 295 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 135 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 160 outliers final: 152 residues processed: 10 average time/residue: 0.9348 time to fit residues: 14.8371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.252 17206 Z= 3.167 Angle : 1.906 12.880 23310 Z= 1.058 Chirality : 0.168 1.510 2772 Planarity : 0.013 0.101 2926 Dihedral : 14.746 136.476 2653 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 53.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.46 % Favored : 80.54 % Rotamer: Outliers : 15.37 % Allowed : 20.95 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.03 (0.13), residues: 1778 helix: -3.74 (0.11), residues: 973 sheet: -3.10 (0.27), residues: 259 loop : -4.47 (0.16), residues: 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 134 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 240 outliers final: 172 residues processed: 350 average time/residue: 1.2763 time to fit residues: 549.7130 Evaluate side-chains 303 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 131 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 167 residues processed: 6 average time/residue: 0.6812 time to fit residues: 8.8310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.251 17206 Z= 3.168 Angle : 1.910 12.787 23310 Z= 1.059 Chirality : 0.167 1.505 2772 Planarity : 0.013 0.102 2926 Dihedral : 14.625 130.122 2653 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 54.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.47 % Favored : 79.53 % Rotamer: Outliers : 15.12 % Allowed : 22.49 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.05 (0.13), residues: 1778 helix: -3.70 (0.11), residues: 945 sheet: -3.16 (0.26), residues: 259 loop : -4.59 (0.15), residues: 574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 136 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 236 outliers final: 185 residues processed: 355 average time/residue: 1.2787 time to fit residues: 563.0397 Evaluate side-chains 320 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 135 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 179 residues processed: 9 average time/residue: 0.7046 time to fit residues: 11.9556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.168 Angle : 1.912 12.849 23310 Z= 1.060 Chirality : 0.167 1.521 2772 Planarity : 0.013 0.104 2926 Dihedral : 14.476 112.792 2653 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 56.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.58 % Favored : 79.42 % Rotamer: Outliers : 14.93 % Allowed : 23.19 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.06 (0.13), residues: 1778 helix: -3.69 (0.11), residues: 952 sheet: -3.19 (0.26), residues: 259 loop : -4.60 (0.15), residues: 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 134 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 193 residues processed: 348 average time/residue: 1.2112 time to fit residues: 521.8792 Evaluate side-chains 326 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 133 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 193 outliers final: 181 residues processed: 14 average time/residue: 0.6764 time to fit residues: 16.3071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.251 17206 Z= 3.168 Angle : 1.917 12.664 23310 Z= 1.062 Chirality : 0.168 1.510 2772 Planarity : 0.013 0.105 2926 Dihedral : 14.429 111.447 2653 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 56.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.87 % Favored : 79.13 % Rotamer: Outliers : 14.22 % Allowed : 24.09 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.08 (0.13), residues: 1778 helix: -3.69 (0.11), residues: 952 sheet: -3.20 (0.26), residues: 259 loop : -4.64 (0.15), residues: 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 133 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 222 outliers final: 187 residues processed: 336 average time/residue: 1.3523 time to fit residues: 571.8206 Evaluate side-chains 313 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 126 time to evaluate : 2.685 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 181 residues processed: 7 average time/residue: 0.8130 time to fit residues: 11.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.169 Angle : 1.917 12.700 23310 Z= 1.062 Chirality : 0.168 1.514 2772 Planarity : 0.013 0.105 2926 Dihedral : 14.397 108.807 2653 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 57.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.09 % Favored : 78.91 % Rotamer: Outliers : 13.26 % Allowed : 25.24 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -6.10 (0.13), residues: 1778 helix: -3.72 (0.11), residues: 952 sheet: -3.20 (0.26), residues: 259 loop : -4.63 (0.15), residues: 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 127 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 187 residues processed: 320 average time/residue: 1.2630 time to fit residues: 498.5725 Evaluate side-chains 313 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 126 time to evaluate : 2.509 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 181 residues processed: 7 average time/residue: 0.4516 time to fit residues: 8.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.060298 restraints weight = 113293.415| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.54 r_work: 0.2687 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.250 17206 Z= 3.168 Angle : 1.919 12.751 23310 Z= 1.062 Chirality : 0.168 1.516 2772 Planarity : 0.013 0.105 2926 Dihedral : 14.393 108.510 2653 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 57.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.60 % Favored : 78.40 % Rotamer: Outliers : 13.00 % Allowed : 25.50 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.10 (0.13), residues: 1778 helix: -3.71 (0.11), residues: 952 sheet: -3.19 (0.26), residues: 259 loop : -4.65 (0.15), residues: 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14309.82 seconds wall clock time: 250 minutes 40.33 seconds (15040.33 seconds total)