Starting phenix.real_space_refine (version: dev) on Wed Apr 6 13:30:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.275 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/04_2022/3j9j_5778.pdb" } resolution = 3.275 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 21068 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 308, 'PCIS': 1} Chain: "B" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 308, 'PCIS': 1} Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 308, 'PCIS': 1} Chain: "D" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 308, 'PCIS': 1} Time building chain proxies: 10.07, per 1000 atoms: 0.48 Number of scatterers: 21068 At special positions: 0 Unit cell: (117.913, 117.913, 82.6608, 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) S 80 16.00 O 1804 8.00 N 1608 7.00 C 6952 6.00 H 10624 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 74 Processing helix chain 'A' and resid 88 through 119 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.772A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 74 Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 130 through 152 removed outlier: 4.390A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.850A pdb=" N PHE B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 287 through 309 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 49 through 74 Processing helix chain 'C' and resid 88 through 119 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 206 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.852A pdb=" N PHE C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 268 Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 287 through 309 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 49 through 74 Processing helix chain 'D' and resid 88 through 119 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 130 through 152 removed outlier: 4.392A pdb=" N PHE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 206 " --> pdb=" O PHE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 268 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 287 through 309 760 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 19.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10600 1.13 - 1.30: 1564 1.30 - 1.47: 4509 1.47 - 1.64: 4515 1.64 - 1.81: 136 Bond restraints: 21324 Sorted by residual: bond pdb=" CE1 HIS A 30 " pdb=" HE1 HIS A 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 HIS C 30 " pdb=" HE1 HIS C 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 TYR B 131 " pdb=" HE1 TYR B 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" CE1 TYR A 131 " pdb=" HE1 TYR A 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CZ2 TRP C 294 " pdb=" HZ2 TRP C 294 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.29: 120 103.29 - 110.89: 22012 110.89 - 118.48: 5119 118.48 - 126.08: 11102 126.08 - 133.68: 79 Bond angle restraints: 38432 Sorted by residual: angle pdb=" C ARG B 120 " pdb=" N PRO B 121 " pdb=" CA PRO B 121 " ideal model delta sigma weight residual 119.28 127.05 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" C ARG D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta sigma weight residual 119.28 127.04 -7.76 1.10e+00 8.26e-01 4.98e+01 angle pdb=" C ARG A 120 " pdb=" N PRO A 121 " pdb=" CA PRO A 121 " ideal model delta sigma weight residual 119.28 127.01 -7.73 1.10e+00 8.26e-01 4.93e+01 angle pdb=" C ARG C 120 " pdb=" N PRO C 121 " pdb=" CA PRO C 121 " ideal model delta sigma weight residual 119.28 126.97 -7.69 1.10e+00 8.26e-01 4.89e+01 angle pdb=" C LEU D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.03e+00 9.43e-01 4.50e+01 ... (remaining 38427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 8265 13.30 - 26.61: 283 26.61 - 39.91: 48 39.91 - 53.21: 30 53.21 - 66.51: 110 Dihedral angle restraints: 8736 sinusoidal: 3948 harmonic: 4788 Sorted by residual: dihedral pdb=" CB MET D 182 " pdb=" CG MET D 182 " pdb=" SD MET D 182 " pdb=" CE MET D 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.64 -39.64 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET C 182 " pdb=" CG MET C 182 " pdb=" SD MET C 182 " pdb=" CE MET C 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.63 -39.63 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET A 182 " pdb=" CG MET A 182 " pdb=" SD MET A 182 " pdb=" CE MET A 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.62 -39.62 3 1.50e+01 4.44e-03 7.03e+00 ... (remaining 8733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 566 0.047 - 0.093: 570 0.093 - 0.140: 323 0.140 - 0.186: 106 0.186 - 0.233: 59 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA PHE A 309 " pdb=" N PHE A 309 " pdb=" C PHE A 309 " pdb=" CB PHE A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE B 309 " pdb=" N PHE B 309 " pdb=" C PHE B 309 " pdb=" CB PHE B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PHE D 309 " pdb=" N PHE D 309 " pdb=" C PHE D 309 " pdb=" CB PHE D 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1621 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 30 " 0.057 2.00e-02 2.50e+03 4.44e-02 4.43e+01 pdb=" CG HIS D 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS D 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS D 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS D 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS D 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS D 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS D 30 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 30 " -0.057 2.00e-02 2.50e+03 4.43e-02 4.42e+01 pdb=" CG HIS A 30 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS A 30 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 30 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 30 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 30 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS A 30 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS A 30 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 30 " 0.057 2.00e-02 2.50e+03 4.42e-02 4.40e+01 pdb=" CG HIS B 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS B 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS B 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS B 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 30 " 0.042 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 710 2.01 - 2.66: 28402 2.66 - 3.30: 66390 3.30 - 3.95: 84546 3.95 - 4.60: 128117 Nonbonded interactions: 308165 Sorted by model distance: nonbonded pdb=" OE1 GLU D 156 " pdb=" H GLU D 156 " model vdw 1.360 1.850 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.360 1.850 nonbonded pdb=" OE1 GLU C 156 " pdb=" H GLU C 156 " model vdw 1.360 1.850 nonbonded pdb=" OE1 GLU A 156 " pdb=" H GLU A 156 " model vdw 1.360 1.850 nonbonded pdb=" OE1 GLU A 11 " pdb=" H GLU A 11 " model vdw 1.522 1.850 ... (remaining 308160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 6952 2.51 5 N 1608 2.21 5 O 1804 1.98 5 H 10624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.320 Extract box with map and model: 5.660 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.180 Process input model: 66.620 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 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 : 0.015 0.063 10700 Z= 0.947 Angle : 1.078 9.580 14452 Z= 0.764 Chirality : 0.089 0.233 1624 Planarity : 0.010 0.126 1756 Dihedral : 9.349 66.513 3880 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 2.24 % Allowed : 3.27 % Favored : 94.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.65 (0.22), residues: 1252 helix: -0.21 (0.15), residues: 964 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.5075 time to fit residues: 370.5087 Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10700 Z= 0.224 Angle : 0.591 4.623 14452 Z= 0.333 Chirality : 0.036 0.141 1624 Planarity : 0.005 0.068 1756 Dihedral : 4.095 22.159 1408 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.99 % Favored : 93.37 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.29 (0.23), residues: 1252 helix: 1.27 (0.15), residues: 944 sheet: None (None), residues: 0 loop : -0.24 (0.41), residues: 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 379 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 387 average time/residue: 0.4458 time to fit residues: 248.4979 Evaluate side-chains 311 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 297 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3717 time to fit residues: 9.9539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 10700 Z= 0.269 Angle : 0.569 4.391 14452 Z= 0.321 Chirality : 0.035 0.135 1624 Planarity : 0.004 0.057 1756 Dihedral : 4.120 25.667 1408 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.55 % Favored : 92.81 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1252 helix: 1.76 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 334 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 341 average time/residue: 0.4561 time to fit residues: 225.7929 Evaluate side-chains 323 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 305 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2770 time to fit residues: 10.9238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10700 Z= 0.257 Angle : 0.545 4.458 14452 Z= 0.307 Chirality : 0.035 0.133 1624 Planarity : 0.004 0.055 1756 Dihedral : 4.127 26.854 1408 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.71 % Favored : 92.65 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.86 (0.23), residues: 1252 helix: 1.88 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 332 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 336 average time/residue: 0.4363 time to fit residues: 215.4312 Evaluate side-chains 308 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 301 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2988 time to fit residues: 5.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.5830 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10700 Z= 0.247 Angle : 0.539 5.263 14452 Z= 0.302 Chirality : 0.035 0.135 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.110 26.742 1408 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.11 % Favored : 92.33 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.81 (0.23), residues: 1252 helix: 1.92 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.45 (0.36), residues: 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 313 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 316 average time/residue: 0.4181 time to fit residues: 194.7721 Evaluate side-chains 298 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 293 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2421 time to fit residues: 4.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10700 Z= 0.179 Angle : 0.513 4.669 14452 Z= 0.281 Chirality : 0.034 0.140 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.012 26.329 1408 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.95 % Favored : 92.49 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1252 helix: 2.18 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 309 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 310 average time/residue: 0.4102 time to fit residues: 187.9877 Evaluate side-chains 296 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 290 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2884 time to fit residues: 5.0353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 10700 Z= 0.290 Angle : 0.567 5.184 14452 Z= 0.318 Chirality : 0.036 0.165 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.061 28.016 1408 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.19 % Favored : 92.25 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.84 (0.23), residues: 1252 helix: 2.04 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 296 average time/residue: 0.4017 time to fit residues: 177.8516 Evaluate side-chains 288 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 277 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2395 time to fit residues: 6.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.5834 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10700 Z= 0.211 Angle : 0.558 6.896 14452 Z= 0.302 Chirality : 0.036 0.162 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.025 27.341 1408 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.03 % Favored : 92.41 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.24), residues: 1252 helix: 2.19 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -1.82 (0.34), residues: 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 287 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 288 average time/residue: 0.4109 time to fit residues: 174.8599 Evaluate side-chains 278 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2212 time to fit residues: 2.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10700 Z= 0.183 Angle : 0.558 7.638 14452 Z= 0.300 Chirality : 0.036 0.145 1624 Planarity : 0.004 0.054 1756 Dihedral : 3.940 26.441 1408 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.79 % Favored : 92.65 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1252 helix: 2.34 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -1.68 (0.35), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 297 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 299 average time/residue: 0.4167 time to fit residues: 184.0714 Evaluate side-chains 287 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 1.726 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2441 time to fit residues: 4.3285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10700 Z= 0.220 Angle : 0.590 8.954 14452 Z= 0.317 Chirality : 0.037 0.173 1624 Planarity : 0.004 0.054 1756 Dihedral : 3.967 26.859 1408 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.35 % Favored : 92.09 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.24), residues: 1252 helix: 2.25 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 287 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 288 average time/residue: 0.4132 time to fit residues: 176.4191 Evaluate side-chains 279 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2215 time to fit residues: 2.9876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.0670 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.082866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070052 restraints weight = 110746.790| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.38 r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work: 0.3169 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work: 0.3157 rms_B_bonded: 4.13 restraints_weight: 0.0625 r_work: 0.3145 rms_B_bonded: 4.26 restraints_weight: 0.0312 r_work: 0.3132 rms_B_bonded: 4.42 restraints_weight: 0.0156 r_work: 0.3119 rms_B_bonded: 4.63 restraints_weight: 0.0078 r_work: 0.3105 rms_B_bonded: 4.87 restraints_weight: 0.0039 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10700 Z= 0.178 Angle : 0.576 8.848 14452 Z= 0.306 Chirality : 0.036 0.179 1624 Planarity : 0.003 0.054 1756 Dihedral : 3.914 25.177 1408 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.71 % Favored : 92.73 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.24), residues: 1252 helix: 2.33 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 284 =============================================================================== Job complete usr+sys time: 4758.62 seconds wall clock time: 85 minutes 6.49 seconds (5106.49 seconds total)