Starting phenix.real_space_refine on Sat Jan 20 01:40:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5n_20650/01_2024/6u5n_20650.pdb" } resolution = 3.2 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= 0.006 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: 5 Type Number sf(0) Gaussians Ca 24 9.91 5 S 56 5.16 5 C 8302 2.51 5 N 2374 2.21 5 O 2506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 244": "OD1" <-> "OD2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G ASP 226": "OD1" <-> "OD2" Residue "G PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H ARG 262": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13262 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 1662 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 222, 1651 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 1660 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1654 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1647 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 241 " occ=0.50 residue: pdb=" N AARG C 241 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 241 " occ=0.50 Time building chain proxies: 8.76, per 1000 atoms: 0.66 Number of scatterers: 13262 At special positions: 0 Unit cell: (141.384, 137, 69.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 24 19.99 S 56 16.00 O 2506 8.00 N 2374 7.00 C 8302 6.00 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: 5.27 Conformation dependent library (CDL) restraints added in 3.3 seconds 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 45.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.617A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.627A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.559A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET F 250 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.565A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.623A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.530A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 246 through 256 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.521A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.566A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.659A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.616A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 removed outlier: 3.586A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.799A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.594A pdb=" N VAL G 288 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.512A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.582A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.555A pdb=" N VAL D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 155 removed outlier: 3.857A pdb=" N SER H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.637A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.628A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.558A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.596A pdb=" N MET H 250 " --> pdb=" O GLY H 246 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.689A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.566A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.501A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.552A pdb=" N ALA E 143 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 301 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.402A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS F 117 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 180 " --> pdb=" O HIS F 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.500A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.551A pdb=" N ALA G 143 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.515A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.401A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 7.185A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.482A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS H 117 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 180 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.258A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4523 1.34 - 1.45: 1252 1.45 - 1.57: 7537 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 13400 Sorted by residual: bond pdb=" N PRO C 324 " pdb=" CD PRO C 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" N PRO A 324 " pdb=" CD PRO A 324 " ideal model delta sigma weight residual 1.473 1.408 0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" CA GLU B 212 " pdb=" C GLU B 212 " ideal model delta sigma weight residual 1.524 1.556 -0.033 1.26e-02 6.30e+03 6.69e+00 bond pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.26e-02 6.30e+03 6.63e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.03e+00 ... (remaining 13395 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 256 106.29 - 113.22: 7629 113.22 - 120.15: 4709 120.15 - 127.09: 5466 127.09 - 134.02: 92 Bond angle restraints: 18152 Sorted by residual: angle pdb=" N ARG D 298 " pdb=" CA ARG D 298 " pdb=" C ARG D 298 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.50e+01 angle pdb=" N ARG B 298 " pdb=" CA ARG B 298 " pdb=" C ARG B 298 " ideal model delta sigma weight residual 109.07 118.56 -9.49 1.61e+00 3.86e-01 3.47e+01 angle pdb=" N PRO A 324 " pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N PRO C 324 " pdb=" CA PRO C 324 " pdb=" C PRO C 324 " ideal model delta sigma weight residual 113.65 119.91 -6.26 1.35e+00 5.49e-01 2.15e+01 angle pdb=" N GLU D 212 " pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 111.14 115.20 -4.06 1.08e+00 8.57e-01 1.42e+01 ... (remaining 18147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 7345 17.29 - 34.58: 679 34.58 - 51.87: 106 51.87 - 69.16: 36 69.16 - 86.45: 14 Dihedral angle restraints: 8180 sinusoidal: 3108 harmonic: 5072 Sorted by residual: dihedral pdb=" CA ASP G 284 " pdb=" C ASP G 284 " pdb=" N ILE G 285 " pdb=" CA ILE G 285 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP E 284 " pdb=" C ASP E 284 " pdb=" N ILE E 285 " pdb=" CA ILE E 285 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP G 245 " pdb=" C ASP G 245 " pdb=" N GLY G 246 " pdb=" CA GLY G 246 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1456 0.047 - 0.095: 470 0.095 - 0.142: 223 0.142 - 0.189: 19 0.189 - 0.237: 6 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CA PRO C 324 " pdb=" N PRO C 324 " pdb=" C PRO C 324 " pdb=" CB PRO C 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL B 278 " pdb=" CA VAL B 278 " pdb=" CG1 VAL B 278 " pdb=" CG2 VAL B 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2171 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 323 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO D 324 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 323 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO B 324 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 267 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO D 268 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.027 5.00e-02 4.00e+02 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 83 2.51 - 3.10: 8642 3.10 - 3.70: 19374 3.70 - 4.30: 28296 4.30 - 4.90: 49370 Nonbonded interactions: 105765 Sorted by model distance: nonbonded pdb=" O ASP C 244 " pdb=" OD1 ASP C 245 " model vdw 1.907 3.040 nonbonded pdb=" O ASP A 244 " pdb=" OD1 ASP A 245 " model vdw 1.907 3.040 nonbonded pdb=" O GLY E 290 " pdb="CA CA E 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY G 290 " pdb="CA CA G 402 " model vdw 2.034 2.510 nonbonded pdb=" O GLY C 290 " pdb="CA CA C 403 " model vdw 2.058 2.510 ... (remaining 105760 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' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'B' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'C' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA o \ r name C or name O or name CB )) or resid 136 through 137 or (resid 138 and (nam \ e N or name CA or name C or name O or name CB )) or resid 139 through 143 or (re \ sid 144 and (name N or name CA or name C or name O or name CB )) or resid 145 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 170 or (resid 171 and (name N or name CA or name C or name \ O or name CB )) or resid 172 through 240 or resid 242 through 244 or (resid 245 \ and (name N or name CA or name C or name O or name CB )) or resid 246 through 2 \ 53 or (resid 254 and (name N or name CA or name C or name O or name CB )) or res \ id 255 through 262 or (resid 263 and (name N or name CA or name C or name O or n \ ame CB )) or resid 264 through 273 or (resid 274 and (name N or name CA or name \ C or name O or name CB )) or resid 275 through 283 or (resid 284 and (name N or \ name CA or name C or name O or name CB )) or resid 285 through 286 or (resid 287 \ and (name N or name CA or name C or name O or name CB )) or resid 288 through 2 \ 97 or (resid 298 and (name N or name CA or name C or name O or name CB )) or res \ id 299 through 312 or (resid 313 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 through 324 or (resid 325 and (name N or name \ CA or name C or name O or name CB )) or resid 326 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 336 o \ r resid 401 through 402)) selection = (chain 'D' and (resid 115 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 137 or (resid 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 or (resid 149 through 150 and (name N or name CA or name C or name O o \ r name CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 240 or resid 2 \ 42 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB )) or resid 255 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 and (name N or name \ CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N or \ name CA or name C or name O or name CB )) or resid 277 through 280 or (resid 281 \ through 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 297 or (resid 298 and (name N or name CA or name C or name O or name \ CB )) or resid 299 through 312 or (resid 313 through 314 and (name N or name CA \ or name C or name O or name CB )) or resid 315 through 336 or resid 401 through \ 402)) selection = (chain 'E' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'F' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) selection = (chain 'G' and (resid 115 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 148 or (resid 149 through 150 \ and (name N or name CA or name C or name O or name CB )) or resid 151 through 15 \ 3 or (resid 154 and (name N or name CA or name C or name O or name CB )) or resi \ d 155 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 240 or resid 242 t \ hrough 243 or (resid 244 through 245 and (name N or name CA or name C or name O \ or name CB )) or resid 246 through 253 or (resid 254 and (name N or name CA or n \ ame C or name O or name CB )) or resid 255 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 281 or (resid \ 282 through 284 and (name N or name CA or name C or name O or name CB )) or res \ id 285 through 300 or (resid 301 and (name N or name CA or name C or name O or n \ ame CB )) or resid 302 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 312 or (resid 313 through 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 324 o \ r (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 26 through 336 or resid 401 through 402)) selection = (chain 'H' and (resid 115 through 143 or (resid 144 and (name N or name CA or na \ me C or name O or name CB )) or resid 145 or (resid 146 through 147 and (name N \ or name CA or name C or name O or name CB )) or resid 148 or (resid 149 through \ 150 and (name N or name CA or name C or name O or name CB )) or resid 151 throug \ h 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) or \ resid 155 through 217 or (resid 218 and (name N or name CA or name C or name O o \ r name CB )) or resid 219 through 240 or resid 242 through 243 or (resid 244 thr \ ough 245 and (name N or name CA or name C or name O or name CB )) or resid 246 t \ hrough 280 or (resid 281 through 284 and (name N or name CA or name C or name O \ or name CB )) or resid 285 through 286 or (resid 287 and (name N or name CA or n \ ame C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 or (resid 300 through \ 301 and (name N or name CA or name C or name O or name CB )) or resid 302 throu \ gh 307 or (resid 308 through 309 and (name N or name CA or name C or name O or n \ ame CB )) or resid 310 through 324 or (resid 325 and (name N or name CA or name \ C or name O or name CB )) or resid 326 through 327 or (resid 328 and (name N or \ name CA or name C or name O or name CB )) or resid 329 through 336 or resid 401 \ through 402)) } 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=0.50 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.540 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.990 Find NCS groups from input model: 1.110 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.006 0.068 13400 Z= 0.394 Angle : 0.759 9.527 18152 Z= 0.466 Chirality : 0.055 0.237 2174 Planarity : 0.005 0.055 2360 Dihedral : 14.130 86.454 4912 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.15 % Allowed : 5.95 % Favored : 93.90 % 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: -3.09 (0.16), residues: 1766 helix: -2.90 (0.12), residues: 838 sheet: 1.11 (0.27), residues: 304 loop : -2.23 (0.18), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 123 HIS 0.013 0.002 HIS E 193 PHE 0.010 0.002 PHE C 232 TYR 0.011 0.002 TYR E 247 ARG 0.003 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8941 (mm) cc_final: 0.8610 (mm) REVERT: E 184 ASP cc_start: 0.8009 (t0) cc_final: 0.7693 (t0) REVERT: E 294 ILE cc_start: 0.8905 (pt) cc_final: 0.8666 (pt) REVERT: E 317 ILE cc_start: 0.9106 (mm) cc_final: 0.8887 (mm) REVERT: E 323 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7684 (mtpp) REVERT: B 172 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8033 (mtpt) REVERT: B 303 ILE cc_start: 0.8565 (mt) cc_final: 0.8288 (mm) REVERT: F 218 GLU cc_start: 0.7598 (pt0) cc_final: 0.7345 (pt0) REVERT: C 317 ILE cc_start: 0.8963 (mm) cc_final: 0.8673 (mm) REVERT: G 184 ASP cc_start: 0.7993 (t0) cc_final: 0.7690 (t0) REVERT: G 247 TYR cc_start: 0.8825 (m-80) cc_final: 0.8343 (m-80) REVERT: G 294 ILE cc_start: 0.8894 (pt) cc_final: 0.8657 (pt) REVERT: G 317 ILE cc_start: 0.9045 (mm) cc_final: 0.8781 (mm) REVERT: D 172 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8054 (mtpt) REVERT: D 184 ASP cc_start: 0.8135 (t0) cc_final: 0.7740 (t70) REVERT: D 285 ILE cc_start: 0.8922 (mm) cc_final: 0.8717 (mm) REVERT: D 303 ILE cc_start: 0.8544 (mt) cc_final: 0.8270 (mm) REVERT: D 333 TYR cc_start: 0.8695 (t80) cc_final: 0.8482 (t80) REVERT: H 218 GLU cc_start: 0.7676 (pt0) cc_final: 0.7425 (pt0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3819 time to fit residues: 157.6578 Evaluate side-chains 248 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13400 Z= 0.159 Angle : 0.426 3.362 18152 Z= 0.233 Chirality : 0.046 0.138 2174 Planarity : 0.004 0.037 2360 Dihedral : 3.607 13.507 1942 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.09 % Allowed : 10.45 % Favored : 88.46 % 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: -1.39 (0.18), residues: 1766 helix: -1.10 (0.17), residues: 846 sheet: 1.15 (0.27), residues: 304 loop : -1.56 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 123 HIS 0.004 0.001 HIS E 193 PHE 0.005 0.001 PHE A 232 TYR 0.017 0.001 TYR B 333 ARG 0.006 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8887 (mm) cc_final: 0.8539 (mm) REVERT: E 184 ASP cc_start: 0.7871 (t0) cc_final: 0.7548 (t0) REVERT: E 323 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7475 (mtpp) REVERT: B 172 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7894 (mtpt) REVERT: B 218 GLU cc_start: 0.7826 (tp30) cc_final: 0.7615 (tp30) REVERT: B 303 ILE cc_start: 0.8422 (mt) cc_final: 0.8092 (mm) REVERT: F 218 GLU cc_start: 0.7553 (pt0) cc_final: 0.7339 (pt0) REVERT: F 245 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7268 (p0) REVERT: C 221 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7897 (mtm-85) REVERT: C 317 ILE cc_start: 0.8901 (mm) cc_final: 0.8558 (mm) REVERT: G 184 ASP cc_start: 0.7865 (t0) cc_final: 0.7557 (t0) REVERT: D 172 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7938 (mtpt) REVERT: D 303 ILE cc_start: 0.8411 (mt) cc_final: 0.8087 (mm) REVERT: H 245 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7188 (p0) outliers start: 13 outliers final: 7 residues processed: 269 average time/residue: 0.3387 time to fit residues: 121.6863 Evaluate side-chains 236 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 128 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN C 227 GLN C 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13400 Z= 0.168 Angle : 0.401 3.186 18152 Z= 0.217 Chirality : 0.046 0.136 2174 Planarity : 0.003 0.034 2360 Dihedral : 3.367 12.235 1942 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.67 % Allowed : 11.83 % Favored : 86.50 % 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: -0.56 (0.19), residues: 1766 helix: -0.31 (0.18), residues: 846 sheet: 1.18 (0.27), residues: 304 loop : -1.09 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 123 HIS 0.004 0.001 HIS E 193 PHE 0.006 0.001 PHE C 232 TYR 0.019 0.001 TYR D 333 ARG 0.004 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 184 ASP cc_start: 0.7892 (t0) cc_final: 0.7590 (t0) REVERT: E 210 GLU cc_start: 0.7731 (tt0) cc_final: 0.7421 (tt0) REVERT: E 247 TYR cc_start: 0.8515 (m-80) cc_final: 0.8029 (m-80) REVERT: B 172 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7879 (mtpt) REVERT: B 303 ILE cc_start: 0.8324 (mt) cc_final: 0.8108 (mm) REVERT: B 313 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7242 (mtm180) REVERT: F 218 GLU cc_start: 0.7591 (pt0) cc_final: 0.7358 (pt0) REVERT: F 245 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7159 (p0) REVERT: G 184 ASP cc_start: 0.7891 (t0) cc_final: 0.7595 (t0) REVERT: G 210 GLU cc_start: 0.7718 (tt0) cc_final: 0.7451 (tt0) REVERT: G 247 TYR cc_start: 0.8581 (m-80) cc_final: 0.8190 (m-80) REVERT: D 172 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7912 (mtpt) REVERT: D 303 ILE cc_start: 0.8327 (mt) cc_final: 0.8095 (mm) REVERT: D 313 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7305 (mtm180) REVERT: H 245 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7162 (p0) outliers start: 21 outliers final: 13 residues processed: 245 average time/residue: 0.3166 time to fit residues: 105.6053 Evaluate side-chains 237 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 309 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13400 Z= 0.465 Angle : 0.534 5.241 18152 Z= 0.281 Chirality : 0.051 0.139 2174 Planarity : 0.004 0.037 2360 Dihedral : 3.806 16.383 1942 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 15.24 % Favored : 82.87 % 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: -0.58 (0.19), residues: 1766 helix: -0.42 (0.18), residues: 838 sheet: 1.04 (0.28), residues: 304 loop : -0.85 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 123 HIS 0.010 0.002 HIS G 193 PHE 0.011 0.002 PHE A 232 TYR 0.012 0.002 TYR H 333 ARG 0.008 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 247 TYR cc_start: 0.8775 (m-80) cc_final: 0.8259 (m-80) REVERT: E 323 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7611 (mtpp) REVERT: B 116 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7719 (mtp85) REVERT: B 172 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7981 (mtpt) REVERT: B 303 ILE cc_start: 0.8422 (mt) cc_final: 0.8217 (mm) REVERT: B 313 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7278 (mtm180) REVERT: F 218 GLU cc_start: 0.7661 (pt0) cc_final: 0.7432 (pt0) REVERT: F 222 MET cc_start: 0.7477 (mtp) cc_final: 0.7233 (mtm) REVERT: F 245 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7110 (p0) REVERT: D 172 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7995 (mtpt) REVERT: D 303 ILE cc_start: 0.8426 (mt) cc_final: 0.8217 (mm) REVERT: D 313 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7297 (mtm180) REVERT: H 245 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7114 (p0) outliers start: 24 outliers final: 20 residues processed: 228 average time/residue: 0.3155 time to fit residues: 97.7138 Evaluate side-chains 231 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 309 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13400 Z= 0.300 Angle : 0.459 4.596 18152 Z= 0.245 Chirality : 0.048 0.147 2174 Planarity : 0.004 0.038 2360 Dihedral : 3.650 14.332 1942 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.89 % Allowed : 15.53 % Favored : 82.58 % 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: -0.28 (0.19), residues: 1766 helix: -0.16 (0.18), residues: 838 sheet: 1.08 (0.28), residues: 304 loop : -0.68 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 123 HIS 0.006 0.001 HIS G 193 PHE 0.009 0.001 PHE C 232 TYR 0.014 0.001 TYR E 333 ARG 0.006 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 221 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7677 (mtmt) REVERT: E 247 TYR cc_start: 0.8713 (m-80) cc_final: 0.8182 (m-80) REVERT: E 323 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7522 (mtpp) REVERT: B 116 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7740 (mtp85) REVERT: B 172 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7921 (mtpt) REVERT: B 303 ILE cc_start: 0.8431 (mt) cc_final: 0.8219 (mm) REVERT: B 313 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7195 (mtm180) REVERT: F 172 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7539 (mtmt) REVERT: F 245 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7129 (p0) REVERT: G 247 TYR cc_start: 0.8754 (m-80) cc_final: 0.8317 (m-80) REVERT: D 172 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7948 (mtpt) REVERT: D 303 ILE cc_start: 0.8431 (mt) cc_final: 0.8220 (mm) REVERT: D 313 ARG cc_start: 0.7541 (mtp85) cc_final: 0.7238 (mtm180) REVERT: H 245 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7134 (p0) outliers start: 24 outliers final: 17 residues processed: 237 average time/residue: 0.3351 time to fit residues: 106.7904 Evaluate side-chains 225 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 309 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 4.9990 chunk 33 optimal weight: 0.0020 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13400 Z= 0.125 Angle : 0.382 3.520 18152 Z= 0.208 Chirality : 0.045 0.135 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.239 11.072 1942 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.45 % Allowed : 16.55 % Favored : 82.00 % 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: 0.24 (0.20), residues: 1766 helix: 0.35 (0.18), residues: 846 sheet: 1.23 (0.29), residues: 304 loop : -0.49 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 123 HIS 0.002 0.000 HIS C 286 PHE 0.006 0.001 PHE E 251 TYR 0.012 0.001 TYR E 333 ARG 0.006 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 172 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7573 (mtmt) REVERT: E 210 GLU cc_start: 0.7637 (tt0) cc_final: 0.7380 (tt0) REVERT: B 116 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7717 (mtp85) REVERT: B 303 ILE cc_start: 0.8469 (mt) cc_final: 0.8265 (mm) REVERT: F 222 MET cc_start: 0.7436 (mtm) cc_final: 0.7205 (mtt) REVERT: F 245 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6995 (p0) REVERT: F 250 MET cc_start: 0.8893 (mtm) cc_final: 0.8673 (mtp) REVERT: F 317 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8465 (mm) REVERT: G 210 GLU cc_start: 0.7644 (tt0) cc_final: 0.7373 (tt0) REVERT: G 250 MET cc_start: 0.8638 (mtt) cc_final: 0.8328 (mtp) REVERT: D 303 ILE cc_start: 0.8448 (mt) cc_final: 0.8230 (mm) REVERT: H 245 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6938 (p0) outliers start: 18 outliers final: 11 residues processed: 236 average time/residue: 0.3435 time to fit residues: 107.6190 Evaluate side-chains 224 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13400 Z= 0.155 Angle : 0.391 4.260 18152 Z= 0.212 Chirality : 0.046 0.135 2174 Planarity : 0.003 0.036 2360 Dihedral : 3.213 11.804 1942 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.38 % Allowed : 17.05 % Favored : 81.57 % 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: 0.46 (0.20), residues: 1766 helix: 0.54 (0.19), residues: 846 sheet: 1.29 (0.29), residues: 304 loop : -0.39 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 123 HIS 0.003 0.000 HIS G 193 PHE 0.007 0.001 PHE C 232 TYR 0.011 0.001 TYR E 333 ARG 0.009 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 116 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7421 (mmm-85) REVERT: B 116 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7799 (mtp85) REVERT: B 303 ILE cc_start: 0.8470 (mt) cc_final: 0.8262 (mm) REVERT: F 245 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6969 (p0) REVERT: F 317 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (mm) REVERT: C 266 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7628 (mt-10) REVERT: G 210 GLU cc_start: 0.7650 (tt0) cc_final: 0.7374 (tt0) REVERT: G 250 MET cc_start: 0.8649 (mtt) cc_final: 0.8342 (mtp) REVERT: D 303 ILE cc_start: 0.8457 (mt) cc_final: 0.8250 (mm) REVERT: H 245 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6912 (p0) REVERT: H 250 MET cc_start: 0.8939 (mtm) cc_final: 0.8683 (mtp) outliers start: 17 outliers final: 12 residues processed: 219 average time/residue: 0.3528 time to fit residues: 103.9072 Evaluate side-chains 215 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13400 Z= 0.162 Angle : 0.391 5.005 18152 Z= 0.210 Chirality : 0.046 0.164 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.207 11.471 1942 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.52 % Allowed : 16.62 % Favored : 81.86 % 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: 0.61 (0.20), residues: 1766 helix: 0.67 (0.19), residues: 846 sheet: 1.37 (0.29), residues: 304 loop : -0.34 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.003 0.000 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.011 0.001 TYR E 333 ARG 0.009 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.541 Fit side-chains REVERT: B 116 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7783 (mtp85) REVERT: B 298 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7749 (mtp180) REVERT: B 303 ILE cc_start: 0.8510 (mt) cc_final: 0.8265 (mm) REVERT: F 245 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6943 (p0) REVERT: F 317 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8476 (mm) REVERT: C 266 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7579 (mt-10) REVERT: G 210 GLU cc_start: 0.7671 (tt0) cc_final: 0.7362 (tt0) REVERT: G 250 MET cc_start: 0.8672 (mtt) cc_final: 0.8363 (mtp) REVERT: D 303 ILE cc_start: 0.8479 (mt) cc_final: 0.8255 (mm) REVERT: D 313 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7252 (mtp180) REVERT: H 245 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6932 (p0) REVERT: H 250 MET cc_start: 0.8941 (mtm) cc_final: 0.8692 (mtp) REVERT: H 317 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8469 (mm) outliers start: 19 outliers final: 14 residues processed: 224 average time/residue: 0.3177 time to fit residues: 96.7556 Evaluate side-chains 221 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.3980 chunk 148 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13400 Z= 0.166 Angle : 0.403 7.561 18152 Z= 0.213 Chirality : 0.046 0.153 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.182 11.403 1942 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 16.55 % Favored : 81.64 % 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: 0.67 (0.20), residues: 1766 helix: 0.73 (0.19), residues: 846 sheet: 1.38 (0.29), residues: 304 loop : -0.30 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.003 0.000 HIS G 193 PHE 0.007 0.001 PHE G 251 TYR 0.010 0.001 TYR E 333 ARG 0.007 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 116 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7762 (mtp85) REVERT: B 303 ILE cc_start: 0.8502 (mt) cc_final: 0.8256 (mm) REVERT: F 245 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7047 (p0) REVERT: F 317 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8478 (mm) REVERT: C 266 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7614 (mt-10) REVERT: G 210 GLU cc_start: 0.7669 (tt0) cc_final: 0.7360 (tt0) REVERT: G 250 MET cc_start: 0.8672 (mtt) cc_final: 0.8367 (mtp) REVERT: D 303 ILE cc_start: 0.8491 (mt) cc_final: 0.8268 (mm) REVERT: D 313 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7270 (mtp180) REVERT: H 245 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7029 (p0) REVERT: H 250 MET cc_start: 0.8932 (mtm) cc_final: 0.8691 (mtp) REVERT: H 317 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8444 (mm) outliers start: 23 outliers final: 18 residues processed: 225 average time/residue: 0.3125 time to fit residues: 95.4787 Evaluate side-chains 230 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13400 Z= 0.142 Angle : 0.395 7.240 18152 Z= 0.209 Chirality : 0.046 0.150 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.132 11.140 1942 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 16.62 % Favored : 81.57 % 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: 0.75 (0.20), residues: 1766 helix: 0.81 (0.19), residues: 846 sheet: 1.41 (0.29), residues: 304 loop : -0.28 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 123 HIS 0.002 0.000 HIS G 193 PHE 0.006 0.001 PHE E 251 TYR 0.010 0.001 TYR E 333 ARG 0.007 0.000 ARG G 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 116 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7753 (mtp85) REVERT: B 303 ILE cc_start: 0.8486 (mt) cc_final: 0.8263 (mm) REVERT: F 245 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7087 (p0) REVERT: F 317 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8475 (mm) REVERT: C 266 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7616 (mt-10) REVERT: G 210 GLU cc_start: 0.7669 (tt0) cc_final: 0.7365 (tt0) REVERT: G 250 MET cc_start: 0.8677 (mtt) cc_final: 0.8376 (mtp) REVERT: D 303 ILE cc_start: 0.8494 (mt) cc_final: 0.8267 (mm) REVERT: D 313 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7176 (mtp180) REVERT: H 245 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7105 (p0) REVERT: H 250 MET cc_start: 0.8923 (mtm) cc_final: 0.8570 (mtp) REVERT: H 317 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8471 (mm) outliers start: 23 outliers final: 19 residues processed: 233 average time/residue: 0.3044 time to fit residues: 96.9518 Evaluate side-chains 235 residues out of total 1518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.146301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110346 restraints weight = 25835.475| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.61 r_work: 0.2789 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13400 Z= 0.216 Angle : 0.428 7.332 18152 Z= 0.225 Chirality : 0.047 0.154 2174 Planarity : 0.003 0.035 2360 Dihedral : 3.251 12.489 1942 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 16.62 % Favored : 81.49 % 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: 0.67 (0.20), residues: 1766 helix: 0.69 (0.19), residues: 846 sheet: 1.43 (0.29), residues: 304 loop : -0.27 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 123 HIS 0.004 0.001 HIS G 193 PHE 0.009 0.001 PHE A 232 TYR 0.009 0.001 TYR E 333 ARG 0.007 0.000 ARG G 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3095.74 seconds wall clock time: 56 minutes 27.65 seconds (3387.65 seconds total)