Starting phenix.real_space_refine on Mon Mar 18 12:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/03_2024/3j9j_5778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/03_2024/3j9j_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_5778/03_2024/3j9j_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/03_2024/3j9j_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/03_2024/3j9j_5778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/03_2024/3j9j_5778.pdb" } resolution = 3.275 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 ------------------------------------------------------------------------------- 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 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. 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-5265/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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Chain: "B" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Chain: "C" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Chain: "D" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Time building chain proxies: 9.62, per 1000 atoms: 0.46 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: 16.86 Conformation dependent library (CDL) restraints added in 1.9 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: 1.76 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: 7.58 Time building geometry restraints manager: 17.42 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: 9433 13.30 - 26.61: 311 26.61 - 39.91: 68 39.91 - 53.21: 98 53.21 - 66.51: 130 Dihedral angle restraints: 10040 sinusoidal: 5252 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 10037 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 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: 1.040 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: 0.310 Extract box with map and model: 4.670 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 66.140 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 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 % Allowed : 0.35 % Favored : 99.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.010 TRP D 294 HIS 0.002 0.001 HIS C 30 PHE 0.023 0.004 PHE A 256 TYR 0.044 0.005 TYR D 250 ARG 0.004 0.001 ARG D 314 *********************** 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 : 1.598 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 REVERT: C 65 MET cc_start: 0.5276 (mmm) cc_final: 0.5068 (mmm) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.5400 time to fit residues: 386.2917 Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN D 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10700 Z= 0.223 Angle : 0.591 4.592 14452 Z= 0.329 Chirality : 0.036 0.142 1624 Planarity : 0.005 0.066 1756 Dihedral : 4.160 22.930 1408 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.99 % Favored : 93.37 % Rotamer: Outliers : 2.52 % Allowed : 11.02 % Favored : 86.46 % 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: 1.32 (0.23), residues: 1252 helix: 1.29 (0.15), residues: 944 sheet: None (None), residues: 0 loop : -0.23 (0.41), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 294 HIS 0.002 0.001 HIS D 30 PHE 0.010 0.001 PHE D 256 TYR 0.010 0.001 TYR A 21 ARG 0.004 0.001 ARG C 75 *********************** 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 422 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 393 time to evaluate : 1.885 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: B 269 ILE cc_start: 0.6200 (mt) cc_final: 0.5708 (mt) REVERT: C 269 ILE cc_start: 0.6113 (mt) cc_final: 0.5663 (mt) REVERT: D 204 TYR cc_start: 0.6178 (t80) cc_final: 0.5944 (t80) outliers start: 29 outliers final: 15 residues processed: 401 average time/residue: 0.4592 time to fit residues: 261.9374 Evaluate side-chains 311 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 296 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN D 118 GLN D 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10700 Z= 0.254 Angle : 0.574 4.486 14452 Z= 0.320 Chirality : 0.035 0.132 1624 Planarity : 0.004 0.056 1756 Dihedral : 4.108 24.764 1408 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.47 % Favored : 92.89 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % 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: 1.87 (0.24), residues: 1252 helix: 1.82 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 294 HIS 0.002 0.001 HIS B 30 PHE 0.014 0.001 PHE C 252 TYR 0.010 0.001 TYR D 185 ARG 0.005 0.000 ARG C 75 *********************** 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 353 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 1.856 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: A 204 TYR cc_start: 0.6221 (t80) cc_final: 0.5834 (t80) REVERT: B 204 TYR cc_start: 0.6176 (t80) cc_final: 0.5878 (t80) REVERT: C 204 TYR cc_start: 0.6188 (t80) cc_final: 0.5963 (t80) REVERT: D 204 TYR cc_start: 0.6375 (t80) cc_final: 0.5948 (t80) outliers start: 32 outliers final: 18 residues processed: 326 average time/residue: 0.4775 time to fit residues: 222.0615 Evaluate side-chains 317 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 299 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.6004 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10700 Z= 0.194 Angle : 0.518 4.391 14452 Z= 0.287 Chirality : 0.034 0.134 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.121 25.160 1408 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.87 % Favored : 92.65 % Rotamer: Outliers : 2.17 % Allowed : 15.45 % Favored : 82.38 % 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: 1.83 (0.23), residues: 1252 helix: 1.85 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 294 HIS 0.001 0.001 HIS A 30 PHE 0.010 0.001 PHE D 202 TYR 0.009 0.001 TYR D 185 ARG 0.006 0.000 ARG B 75 *********************** 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 354 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 329 time to evaluate : 1.852 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: A 204 TYR cc_start: 0.6142 (t80) cc_final: 0.5794 (t80) REVERT: B 204 TYR cc_start: 0.6176 (t80) cc_final: 0.5881 (t80) REVERT: C 204 TYR cc_start: 0.6205 (t80) cc_final: 0.5982 (t80) REVERT: D 118 GLN cc_start: 0.4069 (pt0) cc_final: 0.3850 (pt0) outliers start: 25 outliers final: 13 residues processed: 330 average time/residue: 0.4497 time to fit residues: 213.5740 Evaluate side-chains 316 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 303 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10700 Z= 0.286 Angle : 0.554 4.995 14452 Z= 0.314 Chirality : 0.035 0.125 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.179 26.714 1408 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.35 % Favored : 92.33 % Rotamer: Outliers : 2.17 % Allowed : 17.88 % Favored : 79.95 % 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: 1.74 (0.23), residues: 1252 helix: 1.87 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 294 HIS 0.001 0.001 HIS D 30 PHE 0.010 0.001 PHE D 211 TYR 0.011 0.001 TYR C 61 ARG 0.004 0.000 ARG B 75 *********************** 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 341 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 316 time to evaluate : 1.738 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: D 118 GLN cc_start: 0.4211 (pt0) cc_final: 0.3843 (pt0) outliers start: 25 outliers final: 19 residues processed: 318 average time/residue: 0.4557 time to fit residues: 209.0087 Evaluate side-chains 312 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 293 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 306 GLU 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: 3.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0020 chunk 62 optimal weight: 7.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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: 0.6038 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10700 Z= 0.184 Angle : 0.525 4.701 14452 Z= 0.288 Chirality : 0.035 0.160 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.109 26.473 1408 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.87 % Favored : 92.81 % Rotamer: Outliers : 1.48 % Allowed : 18.84 % Favored : 79.69 % 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: 1.97 (0.24), residues: 1252 helix: 2.07 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 294 HIS 0.001 0.000 HIS D 30 PHE 0.009 0.001 PHE A 202 TYR 0.014 0.001 TYR D 185 ARG 0.005 0.000 ARG B 75 *********************** 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 329 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 312 time to evaluate : 1.651 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: A 204 TYR cc_start: 0.6238 (t80) cc_final: 0.5864 (t80) REVERT: B 204 TYR cc_start: 0.6200 (t80) cc_final: 0.5829 (t80) REVERT: C 204 TYR cc_start: 0.6239 (t80) cc_final: 0.5903 (t80) outliers start: 17 outliers final: 10 residues processed: 312 average time/residue: 0.4325 time to fit residues: 195.3204 Evaluate side-chains 308 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 298 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU 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: 4.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.6873 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= 0.211 Angle : 0.521 4.219 14452 Z= 0.290 Chirality : 0.034 0.159 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.017 27.283 1408 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 1.82 % Allowed : 17.80 % Favored : 80.38 % 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: 2.17 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 294 HIS 0.002 0.001 HIS B 30 PHE 0.011 0.001 PHE A 202 TYR 0.011 0.001 TYR C 61 ARG 0.004 0.000 ARG B 75 *********************** 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 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 303 time to evaluate : 1.816 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: D 118 GLN cc_start: 0.4056 (pt0) cc_final: 0.3844 (pt0) outliers start: 21 outliers final: 13 residues processed: 306 average time/residue: 0.4312 time to fit residues: 191.2130 Evaluate side-chains 303 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10700 Z= 0.229 Angle : 0.543 6.918 14452 Z= 0.299 Chirality : 0.035 0.160 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.017 27.432 1408 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.03 % Favored : 92.65 % Rotamer: Outliers : 2.52 % Allowed : 18.23 % Favored : 79.25 % 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: 2.11 (0.24), residues: 1252 helix: 2.19 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 169 HIS 0.001 0.000 HIS A 30 PHE 0.012 0.001 PHE A 202 TYR 0.011 0.001 TYR A 61 ARG 0.003 0.000 ARG B 177 *********************** 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 317 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 1.621 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: D 118 GLN cc_start: 0.4257 (pt0) cc_final: 0.4014 (pt0) outliers start: 29 outliers final: 16 residues processed: 296 average time/residue: 0.4198 time to fit residues: 182.1309 Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.6041 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10700 Z= 0.180 Angle : 0.551 5.594 14452 Z= 0.299 Chirality : 0.036 0.170 1624 Planarity : 0.004 0.054 1756 Dihedral : 3.952 25.734 1408 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.71 % Favored : 92.97 % Rotamer: Outliers : 1.74 % Allowed : 19.62 % Favored : 78.65 % 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: 2.24 (0.24), residues: 1252 helix: 2.30 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.001 0.000 HIS B 30 PHE 0.012 0.001 PHE A 202 TYR 0.014 0.001 TYR B 185 ARG 0.003 0.000 ARG B 75 *********************** 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 320 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 300 time to evaluate : 1.651 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: A 114 GLN cc_start: 0.4436 (tm-30) cc_final: 0.3608 (tm-30) REVERT: B 114 GLN cc_start: 0.4283 (tm-30) cc_final: 0.3350 (tm-30) REVERT: D 241 MET cc_start: 0.6402 (mmm) cc_final: 0.6115 (mmt) outliers start: 20 outliers final: 11 residues processed: 303 average time/residue: 0.4337 time to fit residues: 190.6279 Evaluate side-chains 292 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 281 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10700 Z= 0.207 Angle : 0.580 6.823 14452 Z= 0.315 Chirality : 0.036 0.168 1624 Planarity : 0.004 0.053 1756 Dihedral : 3.976 25.845 1408 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.95 % Favored : 92.73 % Rotamer: Outliers : 1.74 % Allowed : 21.18 % Favored : 77.08 % 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: 2.17 (0.23), residues: 1252 helix: 2.20 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.001 0.001 HIS C 30 PHE 0.013 0.001 PHE A 202 TYR 0.009 0.001 TYR A 61 ARG 0.004 0.000 ARG B 75 ********************** 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 307 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 287 time to evaluate : 1.706 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: D 241 MET cc_start: 0.6462 (mmm) cc_final: 0.6213 (mmt) outliers start: 20 outliers final: 13 residues processed: 291 average time/residue: 0.4165 time to fit residues: 178.4762 Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 282 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 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 = 0.3476 r_free = 0.3476 target = 0.082368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.069916 restraints weight = 110065.493| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.36 r_work: 0.3077 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10700 Z= 0.216 Angle : 0.574 8.326 14452 Z= 0.313 Chirality : 0.036 0.154 1624 Planarity : 0.004 0.053 1756 Dihedral : 3.954 25.729 1408 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.87 % Favored : 92.81 % Rotamer: Outliers : 1.22 % Allowed : 21.61 % Favored : 77.17 % 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: 2.24 (0.24), residues: 1252 helix: 2.24 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.001 0.000 HIS B 30 PHE 0.014 0.001 PHE A 202 TYR 0.009 0.001 TYR D 61 ARG 0.003 0.000 ARG B 75 =============================================================================== Job complete usr+sys time: 5239.39 seconds wall clock time: 92 minutes 51.34 seconds (5571.34 seconds total)