Starting phenix.real_space_refine on Fri Mar 15 04:04:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amf_15525/03_2024/8amf_15525_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 P 31 5.49 5 S 32 5.16 5 C 6520 2.51 5 N 1798 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 312": "OD1" <-> "OD2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 299": "OD1" <-> "OD2" Residue "G TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G ASP 334": "OD1" <-> "OD2" Residue "G ARG 341": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10507 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2504 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AGS:plan-2': 1, 'AGS:plan-1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 6.06, per 1000 atoms: 0.58 Number of scatterers: 10507 At special positions: 0 Unit cell: (126.48, 119.04, 141.36, 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 32 16.00 P 31 15.00 O 2126 8.00 N 1798 7.00 C 6520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 9 sheets defined 31.6% alpha, 15.2% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.616A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 58 through 61 No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.381A pdb=" N GLU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.529A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 180 through 198 removed outlier: 3.831A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.837A pdb=" N TYR A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.813A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.913A pdb=" N ALA B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 180 through 198 removed outlier: 3.825A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.895A pdb=" N PHE B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.889A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 326 No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.400A pdb=" N ASP B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 335 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.596A pdb=" N ALA F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.675A pdb=" N ALA F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 99 removed outlier: 4.024A pdb=" N ALA F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 135 through 147 removed outlier: 3.619A pdb=" N ASP F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 168 No H-bonds generated for 'chain 'F' and resid 165 through 168' Processing helix chain 'F' and resid 179 through 198 removed outlier: 3.826A pdb=" N LYS F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.566A pdb=" N TYR F 231 " --> pdb=" O ALA F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 231' Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 287 through 298 removed outlier: 3.617A pdb=" N LEU F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 326 No H-bonds generated for 'chain 'F' and resid 323 through 326' Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.731A pdb=" N PHE F 333 " --> pdb=" O PRO F 330 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP F 334 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 335 " --> pdb=" O ILE F 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 330 through 335' Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.528A pdb=" N ALA G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 58 through 61 No H-bonds generated for 'chain 'G' and resid 58 through 61' Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.852A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 120 removed outlier: 3.521A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 148 removed outlier: 4.385A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 165 through 168 No H-bonds generated for 'chain 'G' and resid 165 through 168' Processing helix chain 'G' and resid 180 through 198 removed outlier: 3.996A pdb=" N LYS G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS G 197 " --> pdb=" O ALA G 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 231 removed outlier: 3.737A pdb=" N TYR G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 227 through 231' Processing helix chain 'G' and resid 248 through 250 No H-bonds generated for 'chain 'G' and resid 248 through 250' Processing helix chain 'G' and resid 287 through 297 removed outlier: 4.014A pdb=" N LEU G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 326 No H-bonds generated for 'chain 'G' and resid 323 through 326' Processing helix chain 'G' and resid 330 through 332 No H-bonds generated for 'chain 'G' and resid 330 through 332' Processing helix chain 'G' and resid 334 through 337 No H-bonds generated for 'chain 'G' and resid 334 through 337' Processing sheet with id= A, first strand: chain 'A' and resid 274 through 280 removed outlier: 6.432A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 234 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA A 202 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 77 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 204 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLY A 79 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 130 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 208 through 210 Processing sheet with id= C, first strand: chain 'A' and resid 243 through 248 removed outlier: 6.612A pdb=" N GLY A 246 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN A 254 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY A 248 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 275 through 280 removed outlier: 3.641A pdb=" N VAL B 277 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 235 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA B 202 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE B 77 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE B 204 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY B 79 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 130 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 243 through 248 removed outlier: 6.791A pdb=" N GLY B 246 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 248 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 275 through 280 removed outlier: 3.534A pdb=" N LYS F 262 " --> pdb=" O ASP F 237 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG F 235 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 234 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA F 202 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE F 77 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE F 204 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLY F 79 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 130 " --> pdb=" O PHE F 105 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 243 through 248 removed outlier: 6.637A pdb=" N GLY F 246 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN F 254 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY F 248 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU F 252 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 275 through 280 removed outlier: 6.524A pdb=" N ARG G 235 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL G 234 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA G 202 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE G 77 " --> pdb=" O ALA G 202 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE G 204 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLY G 79 " --> pdb=" O PHE G 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 130 " --> pdb=" O PHE G 105 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 243 through 248 removed outlier: 6.785A pdb=" N GLY G 246 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN G 254 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY G 248 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 3475 1.35 - 1.50: 2611 1.50 - 1.65: 4533 1.65 - 1.80: 45 1.80 - 1.95: 15 Bond restraints: 10679 Sorted by residual: bond pdb=" O1A AGS B 500 " pdb=" PA AGS B 500 " ideal model delta sigma weight residual 1.481 1.582 -0.101 2.70e-02 1.37e+03 1.40e+01 bond pdb=" O2B AGS A 500 " pdb=" PB AGS A 500 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.60e-02 3.91e+03 1.38e+01 bond pdb=" O1A AGS F 500 " pdb=" PA AGS F 500 " ideal model delta sigma weight residual 1.481 1.571 -0.090 2.70e-02 1.37e+03 1.12e+01 bond pdb=" O2B AGS G 500 " pdb=" PB AGS G 500 " ideal model delta sigma weight residual 1.531 1.483 0.048 1.60e-02 3.91e+03 8.81e+00 bond pdb=" O2B AGS B 500 " pdb=" PB AGS B 500 " ideal model delta sigma weight residual 1.531 1.484 0.047 1.60e-02 3.91e+03 8.50e+00 ... (remaining 10674 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.07: 253 105.07 - 112.28: 5254 112.28 - 119.49: 3883 119.49 - 126.70: 4916 126.70 - 133.91: 148 Bond angle restraints: 14454 Sorted by residual: angle pdb=" C LYS B 85 " pdb=" N THR B 86 " pdb=" CA THR B 86 " ideal model delta sigma weight residual 120.68 112.00 8.68 1.70e+00 3.46e-01 2.61e+01 angle pdb=" C LYS F 85 " pdb=" N THR F 86 " pdb=" CA THR F 86 " ideal model delta sigma weight residual 121.52 112.43 9.09 1.84e+00 2.95e-01 2.44e+01 angle pdb=" C ASP B 249 " pdb=" N GLN B 250 " pdb=" CA GLN B 250 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C ASP A 249 " pdb=" N GLN A 250 " pdb=" CA GLN A 250 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASP G 249 " pdb=" N GLN G 250 " pdb=" CA GLN G 250 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 ... (remaining 14449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 6052 28.38 - 56.75: 428 56.75 - 85.13: 51 85.13 - 113.50: 4 113.50 - 141.88: 4 Dihedral angle restraints: 6539 sinusoidal: 2803 harmonic: 3736 Sorted by residual: dihedral pdb=" CA LYS B 14 " pdb=" C LYS B 14 " pdb=" N PHE B 15 " pdb=" CA PHE B 15 " ideal model delta harmonic sigma weight residual 180.00 141.87 38.13 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA GLY G 84 " pdb=" C GLY G 84 " pdb=" N LYS G 85 " pdb=" CA LYS G 85 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLY F 84 " pdb=" C GLY F 84 " pdb=" N LYS F 85 " pdb=" CA LYS F 85 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 6536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1621 0.160 - 0.321: 14 0.321 - 0.481: 0 0.481 - 0.641: 1 0.641 - 0.802: 3 Chirality restraints: 1639 Sorted by residual: chirality pdb=" PB AGS B 500 " pdb=" O2B AGS B 500 " pdb=" O3A AGS B 500 " pdb=" O3B AGS B 500 " both_signs ideal model delta sigma weight residual True 3.18 2.38 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" PB AGS G 500 " pdb=" O2B AGS G 500 " pdb=" O3A AGS G 500 " pdb=" O3B AGS G 500 " both_signs ideal model delta sigma weight residual True 3.18 2.47 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" PB AGS F 500 " pdb=" O2B AGS F 500 " pdb=" O3A AGS F 500 " pdb=" O3B AGS F 500 " both_signs ideal model delta sigma weight residual True 3.18 2.48 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 1636 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 269 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 270 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 269 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO F 270 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 270 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 270 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 269 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO G 270 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 270 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 270 " -0.036 5.00e-02 4.00e+02 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3041 2.80 - 3.33: 9530 3.33 - 3.85: 17086 3.85 - 4.38: 18058 4.38 - 4.90: 30457 Nonbonded interactions: 78172 Sorted by model distance: nonbonded pdb=" OG1 THR A 198 " pdb=" OG1 THR A 200 " model vdw 2.281 2.440 nonbonded pdb=" O1B AGS A 500 " pdb=" O2G AGS A 500 " model vdw 2.315 2.440 nonbonded pdb=" OG1 THR B 198 " pdb=" OG1 THR B 200 " model vdw 2.319 2.440 nonbonded pdb=" O SER A 83 " pdb=" OG SER A 83 " model vdw 2.326 2.440 nonbonded pdb=" OE1 GLU G 31 " pdb=" OG SER G 38 " model vdw 2.327 2.440 ... (remaining 78167 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 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.530 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.260 Find NCS groups from input model: 0.690 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.007 0.143 10679 Z= 0.448 Angle : 0.992 9.496 14454 Z= 0.538 Chirality : 0.065 0.802 1639 Planarity : 0.006 0.075 1800 Dihedral : 18.673 141.876 4163 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.77 % Allowed : 14.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.18), residues: 1324 helix: -2.93 (0.21), residues: 328 sheet: -1.99 (0.31), residues: 212 loop : -2.66 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 307 HIS 0.007 0.001 HIS F 176 PHE 0.021 0.003 PHE B 105 TYR 0.021 0.003 TYR B 78 ARG 0.004 0.000 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9408 (mt) cc_final: 0.8961 (mt) REVERT: A 176 HIS cc_start: 0.7897 (m-70) cc_final: 0.7670 (m90) REVERT: A 183 MET cc_start: 0.9020 (tmm) cc_final: 0.8594 (tmm) REVERT: A 258 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 307 TRP cc_start: 0.8704 (m-90) cc_final: 0.8279 (m-90) REVERT: B 76 GLU cc_start: 0.8000 (pp20) cc_final: 0.7762 (pp20) REVERT: B 183 MET cc_start: 0.8690 (tmm) cc_final: 0.8295 (tmm) REVERT: B 215 MET cc_start: 0.5997 (mmm) cc_final: 0.5779 (mmm) REVERT: B 258 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8016 (tm-30) REVERT: B 274 GLU cc_start: 0.8732 (pp20) cc_final: 0.7907 (pp20) REVERT: F 140 GLU cc_start: 0.8905 (tp30) cc_final: 0.8598 (tp30) REVERT: F 141 ILE cc_start: 0.9301 (mt) cc_final: 0.8909 (mm) REVERT: F 183 MET cc_start: 0.8956 (tmm) cc_final: 0.8332 (tmm) REVERT: F 258 GLU cc_start: 0.8855 (tm-30) cc_final: 0.7791 (tm-30) REVERT: F 274 GLU cc_start: 0.8797 (pp20) cc_final: 0.8490 (pp20) REVERT: F 307 TRP cc_start: 0.8749 (m-90) cc_final: 0.8540 (m-90) REVERT: G 47 GLU cc_start: 0.8930 (pm20) cc_final: 0.8663 (pm20) REVERT: G 183 MET cc_start: 0.8708 (tmm) cc_final: 0.8128 (tmm) REVERT: G 186 GLN cc_start: 0.8691 (tm-30) cc_final: 0.7776 (tp40) REVERT: G 333 PHE cc_start: 0.8006 (m-10) cc_final: 0.7660 (m-80) outliers start: 8 outliers final: 2 residues processed: 187 average time/residue: 0.2207 time to fit residues: 57.9240 Evaluate side-chains 111 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 78 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS B 329 HIS F 176 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10679 Z= 0.299 Angle : 0.675 7.230 14454 Z= 0.364 Chirality : 0.047 0.202 1639 Planarity : 0.004 0.052 1800 Dihedral : 17.001 148.523 1717 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.69 % Allowed : 22.21 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1324 helix: -1.39 (0.26), residues: 340 sheet: -1.55 (0.31), residues: 240 loop : -2.19 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 307 HIS 0.005 0.002 HIS B 329 PHE 0.018 0.002 PHE B 105 TYR 0.022 0.002 TYR A 78 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.7977 (m-70) cc_final: 0.7758 (m90) REVERT: A 183 MET cc_start: 0.9078 (tmm) cc_final: 0.8551 (tmm) REVERT: A 206 ASN cc_start: 0.8443 (t0) cc_final: 0.8200 (t0) REVERT: A 208 LEU cc_start: 0.8853 (tp) cc_final: 0.8419 (tp) REVERT: A 274 GLU cc_start: 0.8842 (pp20) cc_final: 0.8324 (pp20) REVERT: A 283 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8752 (tp30) REVERT: A 315 ILE cc_start: 0.4358 (OUTLIER) cc_final: 0.3558 (mp) REVERT: B 141 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8865 (mp) REVERT: B 183 MET cc_start: 0.8844 (tmm) cc_final: 0.8336 (tmm) REVERT: B 184 MET cc_start: 0.9272 (tpp) cc_final: 0.8950 (tpp) REVERT: B 258 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8559 (tm-30) REVERT: B 274 GLU cc_start: 0.8653 (pp20) cc_final: 0.7803 (pp20) REVERT: F 140 GLU cc_start: 0.8966 (tp30) cc_final: 0.8682 (tp30) REVERT: F 183 MET cc_start: 0.9099 (tmm) cc_final: 0.8272 (tmm) REVERT: F 274 GLU cc_start: 0.9049 (pp20) cc_final: 0.8584 (pp20) REVERT: G 47 GLU cc_start: 0.8937 (pm20) cc_final: 0.8728 (pm20) REVERT: G 183 MET cc_start: 0.8730 (tmm) cc_final: 0.8236 (tmm) REVERT: G 186 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7756 (tp40) REVERT: G 307 TRP cc_start: 0.8352 (m100) cc_final: 0.7403 (m100) REVERT: G 333 PHE cc_start: 0.7971 (m-10) cc_final: 0.7754 (m-80) outliers start: 28 outliers final: 10 residues processed: 152 average time/residue: 0.1741 time to fit residues: 40.5224 Evaluate side-chains 123 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 131 optimal weight: 30.0000 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10679 Z= 0.247 Angle : 0.648 8.638 14454 Z= 0.341 Chirality : 0.046 0.280 1639 Planarity : 0.004 0.044 1800 Dihedral : 16.859 151.089 1717 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.50 % Allowed : 25.00 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.22), residues: 1324 helix: -0.68 (0.28), residues: 340 sheet: -1.15 (0.34), residues: 236 loop : -1.96 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 307 HIS 0.009 0.001 HIS G 329 PHE 0.022 0.001 PHE F 15 TYR 0.018 0.002 TYR A 231 ARG 0.002 0.000 ARG G 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9492 (mt) cc_final: 0.9278 (tp) REVERT: A 176 HIS cc_start: 0.7995 (m-70) cc_final: 0.7721 (m90) REVERT: A 183 MET cc_start: 0.9103 (tmm) cc_final: 0.8526 (tmm) REVERT: A 208 LEU cc_start: 0.8832 (tp) cc_final: 0.8364 (tp) REVERT: A 274 GLU cc_start: 0.8804 (pp20) cc_final: 0.8386 (pp20) REVERT: A 283 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8683 (tp30) REVERT: B 40 MET cc_start: 0.8735 (ptm) cc_final: 0.8213 (ppp) REVERT: B 183 MET cc_start: 0.8848 (tmm) cc_final: 0.8504 (tmm) REVERT: B 184 MET cc_start: 0.9281 (tpp) cc_final: 0.8960 (tpp) REVERT: B 212 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8749 (p) REVERT: B 258 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8612 (tm-30) REVERT: B 274 GLU cc_start: 0.8749 (pp20) cc_final: 0.7916 (pp20) REVERT: F 140 GLU cc_start: 0.8908 (tp30) cc_final: 0.8502 (tp30) REVERT: F 147 ASP cc_start: 0.8235 (p0) cc_final: 0.7513 (t0) REVERT: F 183 MET cc_start: 0.9147 (tmm) cc_final: 0.8330 (tmm) REVERT: F 212 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8185 (p) REVERT: G 183 MET cc_start: 0.8766 (tmm) cc_final: 0.8349 (tmm) REVERT: G 186 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7634 (tp40) REVERT: G 307 TRP cc_start: 0.8574 (m100) cc_final: 0.7563 (m100) REVERT: G 315 ILE cc_start: 0.6359 (OUTLIER) cc_final: 0.6034 (mp) REVERT: G 333 PHE cc_start: 0.7874 (m-10) cc_final: 0.7370 (m-80) outliers start: 26 outliers final: 14 residues processed: 141 average time/residue: 0.1849 time to fit residues: 39.6599 Evaluate side-chains 121 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 0.0040 chunk 115 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10679 Z= 0.252 Angle : 0.640 8.648 14454 Z= 0.337 Chirality : 0.046 0.300 1639 Planarity : 0.004 0.040 1800 Dihedral : 16.671 150.789 1717 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.75 % Allowed : 24.81 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.23), residues: 1324 helix: 0.07 (0.30), residues: 316 sheet: -1.03 (0.33), residues: 240 loop : -1.70 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 307 HIS 0.004 0.001 HIS A 176 PHE 0.011 0.001 PHE B 105 TYR 0.016 0.002 TYR A 78 ARG 0.002 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9495 (mt) cc_final: 0.9287 (tp) REVERT: A 183 MET cc_start: 0.9141 (tmm) cc_final: 0.8556 (tmm) REVERT: A 191 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9270 (mp) REVERT: A 208 LEU cc_start: 0.8898 (tp) cc_final: 0.8624 (tp) REVERT: A 274 GLU cc_start: 0.8813 (pp20) cc_final: 0.8460 (pp20) REVERT: B 40 MET cc_start: 0.8746 (ptm) cc_final: 0.8360 (ppp) REVERT: B 183 MET cc_start: 0.8928 (tmm) cc_final: 0.8581 (tmm) REVERT: B 184 MET cc_start: 0.9267 (tpp) cc_final: 0.8922 (tpp) REVERT: B 212 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8775 (p) REVERT: B 258 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 274 GLU cc_start: 0.8753 (pp20) cc_final: 0.7951 (pp20) REVERT: F 40 MET cc_start: 0.8044 (mtp) cc_final: 0.7830 (ttm) REVERT: F 140 GLU cc_start: 0.8948 (tp30) cc_final: 0.8541 (tp30) REVERT: F 183 MET cc_start: 0.9124 (tmm) cc_final: 0.8319 (tmm) REVERT: F 212 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8279 (p) REVERT: F 274 GLU cc_start: 0.9122 (pp20) cc_final: 0.8056 (pp20) REVERT: G 53 MET cc_start: 0.8815 (tmm) cc_final: 0.8536 (tmm) REVERT: G 183 MET cc_start: 0.8864 (tmm) cc_final: 0.8395 (tmm) REVERT: G 186 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7668 (tp40) REVERT: G 206 ASN cc_start: 0.8862 (t0) cc_final: 0.8575 (t0) REVERT: G 274 GLU cc_start: 0.8862 (pp20) cc_final: 0.8613 (pp20) REVERT: G 333 PHE cc_start: 0.7860 (m-10) cc_final: 0.7372 (m-80) outliers start: 39 outliers final: 20 residues processed: 148 average time/residue: 0.1685 time to fit residues: 38.8241 Evaluate side-chains 136 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 10679 Z= 0.392 Angle : 0.733 8.196 14454 Z= 0.384 Chirality : 0.048 0.245 1639 Planarity : 0.004 0.045 1800 Dihedral : 17.018 151.794 1717 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.33 % Allowed : 26.54 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1324 helix: 0.21 (0.30), residues: 316 sheet: -0.61 (0.35), residues: 228 loop : -1.71 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 307 HIS 0.004 0.001 HIS A 176 PHE 0.025 0.002 PHE G 105 TYR 0.019 0.002 TYR B 310 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 109 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9165 (tmm) cc_final: 0.8561 (tmm) REVERT: A 208 LEU cc_start: 0.8932 (tp) cc_final: 0.8640 (tp) REVERT: A 274 GLU cc_start: 0.9043 (pp20) cc_final: 0.8695 (pp20) REVERT: A 283 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8757 (tp30) REVERT: B 183 MET cc_start: 0.8938 (tmm) cc_final: 0.8525 (tmm) REVERT: B 191 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9295 (mp) REVERT: B 258 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8623 (tm-30) REVERT: F 140 GLU cc_start: 0.8999 (tp30) cc_final: 0.8599 (tp30) REVERT: F 183 MET cc_start: 0.9096 (tmm) cc_final: 0.8228 (tmm) REVERT: F 188 MET cc_start: 0.8804 (tmm) cc_final: 0.8554 (tmm) REVERT: F 251 LYS cc_start: 0.8399 (tptt) cc_final: 0.8026 (tptp) REVERT: F 274 GLU cc_start: 0.9182 (pp20) cc_final: 0.8093 (pp20) REVERT: G 53 MET cc_start: 0.8881 (tmm) cc_final: 0.8489 (tmm) REVERT: G 171 ASP cc_start: 0.8087 (t0) cc_final: 0.7870 (t0) REVERT: G 183 MET cc_start: 0.8848 (tmm) cc_final: 0.8422 (tmm) REVERT: G 206 ASN cc_start: 0.8917 (t0) cc_final: 0.8661 (t0) REVERT: G 251 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7551 (tmtt) REVERT: G 274 GLU cc_start: 0.8959 (pp20) cc_final: 0.8615 (pp20) REVERT: G 307 TRP cc_start: 0.9009 (m100) cc_final: 0.8197 (m100) REVERT: G 315 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.5943 (mt) REVERT: G 333 PHE cc_start: 0.8053 (m-10) cc_final: 0.7526 (m-80) outliers start: 45 outliers final: 30 residues processed: 145 average time/residue: 0.1732 time to fit residues: 38.6674 Evaluate side-chains 137 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 251 LYS Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10679 Z= 0.306 Angle : 0.673 7.919 14454 Z= 0.353 Chirality : 0.047 0.345 1639 Planarity : 0.004 0.039 1800 Dihedral : 16.826 151.423 1717 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.23 % Allowed : 27.50 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1324 helix: 0.13 (0.29), residues: 340 sheet: -0.44 (0.36), residues: 228 loop : -1.72 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 307 HIS 0.006 0.001 HIS A 176 PHE 0.020 0.001 PHE G 105 TYR 0.016 0.002 TYR B 310 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9171 (tmm) cc_final: 0.8593 (tmm) REVERT: A 208 LEU cc_start: 0.8935 (tp) cc_final: 0.8632 (tp) REVERT: A 255 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 274 GLU cc_start: 0.9010 (pp20) cc_final: 0.8733 (pp20) REVERT: A 283 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8751 (tp30) REVERT: B 183 MET cc_start: 0.9002 (tmm) cc_final: 0.8615 (tmm) REVERT: B 212 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8858 (p) REVERT: B 258 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8598 (tm-30) REVERT: F 140 GLU cc_start: 0.9006 (tp30) cc_final: 0.8591 (tp30) REVERT: F 183 MET cc_start: 0.9134 (tmm) cc_final: 0.8292 (tmm) REVERT: G 53 MET cc_start: 0.8907 (tmm) cc_final: 0.8677 (tmm) REVERT: G 171 ASP cc_start: 0.8077 (t0) cc_final: 0.7842 (t0) REVERT: G 183 MET cc_start: 0.8873 (tmm) cc_final: 0.8384 (tmm) REVERT: G 206 ASN cc_start: 0.8900 (t0) cc_final: 0.8642 (t0) REVERT: G 274 GLU cc_start: 0.8977 (pp20) cc_final: 0.8623 (pp20) REVERT: G 307 TRP cc_start: 0.9062 (m100) cc_final: 0.8331 (m100) REVERT: G 315 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.5918 (mt) REVERT: G 333 PHE cc_start: 0.8085 (m-10) cc_final: 0.7561 (m-80) outliers start: 44 outliers final: 33 residues processed: 147 average time/residue: 0.1605 time to fit residues: 36.6465 Evaluate side-chains 143 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10679 Z= 0.174 Angle : 0.605 8.617 14454 Z= 0.317 Chirality : 0.045 0.295 1639 Planarity : 0.004 0.041 1800 Dihedral : 16.305 153.125 1717 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.79 % Allowed : 29.04 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1324 helix: 0.03 (0.29), residues: 364 sheet: -0.23 (0.37), residues: 212 loop : -1.66 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 307 HIS 0.003 0.001 HIS F 176 PHE 0.014 0.001 PHE G 105 TYR 0.014 0.001 TYR G 325 ARG 0.001 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8998 (t80) cc_final: 0.8628 (t80) REVERT: A 141 ILE cc_start: 0.9478 (mt) cc_final: 0.9194 (tp) REVERT: A 157 ASP cc_start: 0.7882 (t0) cc_final: 0.7658 (t0) REVERT: A 183 MET cc_start: 0.9251 (tmm) cc_final: 0.8704 (tmm) REVERT: A 274 GLU cc_start: 0.8859 (pp20) cc_final: 0.8609 (pp20) REVERT: A 283 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8708 (tp30) REVERT: B 40 MET cc_start: 0.8727 (ptp) cc_final: 0.8173 (ppp) REVERT: B 183 MET cc_start: 0.9079 (tmm) cc_final: 0.8804 (tmm) REVERT: B 184 MET cc_start: 0.9102 (tpp) cc_final: 0.8769 (tpp) REVERT: B 212 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8796 (p) REVERT: B 243 GLN cc_start: 0.9263 (pm20) cc_final: 0.9054 (pm20) REVERT: B 258 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8351 (tm-30) REVERT: F 69 TYR cc_start: 0.8906 (m-80) cc_final: 0.8662 (m-80) REVERT: F 76 GLU cc_start: 0.8213 (pp20) cc_final: 0.7868 (pp20) REVERT: F 107 ASP cc_start: 0.6825 (t0) cc_final: 0.6606 (t0) REVERT: F 183 MET cc_start: 0.9160 (tmm) cc_final: 0.8492 (tmm) REVERT: F 206 ASN cc_start: 0.9031 (t0) cc_final: 0.8299 (m-40) REVERT: F 212 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8032 (p) REVERT: G 171 ASP cc_start: 0.7889 (t0) cc_final: 0.7624 (t0) REVERT: G 183 MET cc_start: 0.8975 (tmm) cc_final: 0.8370 (tmm) REVERT: G 206 ASN cc_start: 0.8836 (t0) cc_final: 0.8532 (t0) REVERT: G 255 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8074 (p) REVERT: G 274 GLU cc_start: 0.8872 (pp20) cc_final: 0.8555 (pp20) REVERT: G 307 TRP cc_start: 0.9091 (m100) cc_final: 0.8235 (m100) REVERT: G 315 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.5975 (mt) REVERT: G 325 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7744 (p90) REVERT: G 333 PHE cc_start: 0.7956 (m-10) cc_final: 0.7627 (m-80) outliers start: 29 outliers final: 17 residues processed: 155 average time/residue: 0.1678 time to fit residues: 40.4431 Evaluate side-chains 139 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 10679 Z= 0.333 Angle : 0.703 10.329 14454 Z= 0.364 Chirality : 0.047 0.268 1639 Planarity : 0.004 0.038 1800 Dihedral : 16.618 153.759 1716 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.17 % Allowed : 29.42 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.23), residues: 1324 helix: 0.24 (0.28), residues: 368 sheet: -0.39 (0.36), residues: 236 loop : -1.69 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 307 HIS 0.002 0.001 HIS F 176 PHE 0.020 0.002 PHE B 105 TYR 0.022 0.002 TYR F 231 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9558 (mt) cc_final: 0.9277 (tp) REVERT: A 183 MET cc_start: 0.9176 (tmm) cc_final: 0.8683 (tmm) REVERT: A 274 GLU cc_start: 0.9017 (pp20) cc_final: 0.8719 (pp20) REVERT: A 283 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8662 (tp30) REVERT: B 183 MET cc_start: 0.9055 (tmm) cc_final: 0.8772 (tmm) REVERT: F 76 GLU cc_start: 0.8244 (pp20) cc_final: 0.7902 (pp20) REVERT: F 183 MET cc_start: 0.9109 (tmm) cc_final: 0.8152 (tmm) REVERT: F 251 LYS cc_start: 0.8084 (tptt) cc_final: 0.7593 (tptp) REVERT: F 274 GLU cc_start: 0.9121 (pp20) cc_final: 0.8615 (pp20) REVERT: F 280 MET cc_start: 0.8712 (mmm) cc_final: 0.8275 (mmm) REVERT: G 171 ASP cc_start: 0.7864 (t0) cc_final: 0.7640 (t0) REVERT: G 183 MET cc_start: 0.8923 (tmm) cc_final: 0.8405 (tmm) REVERT: G 206 ASN cc_start: 0.8924 (t0) cc_final: 0.8660 (t0) REVERT: G 274 GLU cc_start: 0.8986 (pp20) cc_final: 0.8621 (pp20) REVERT: G 280 MET cc_start: 0.9011 (mmm) cc_final: 0.8544 (mmm) REVERT: G 307 TRP cc_start: 0.9131 (m100) cc_final: 0.8290 (m100) REVERT: G 315 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.5858 (mt) REVERT: G 333 PHE cc_start: 0.8063 (m-10) cc_final: 0.7696 (m-80) outliers start: 33 outliers final: 24 residues processed: 141 average time/residue: 0.1714 time to fit residues: 37.4688 Evaluate side-chains 136 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 315 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10679 Z= 0.262 Angle : 0.679 12.129 14454 Z= 0.349 Chirality : 0.047 0.268 1639 Planarity : 0.004 0.040 1800 Dihedral : 16.599 155.678 1716 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.27 % Allowed : 29.23 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1324 helix: 0.59 (0.29), residues: 344 sheet: -0.29 (0.36), residues: 236 loop : -1.60 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 307 HIS 0.004 0.001 HIS F 176 PHE 0.018 0.001 PHE G 105 TYR 0.015 0.002 TYR F 231 ARG 0.002 0.000 ARG F 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9536 (mt) cc_final: 0.9253 (tp) REVERT: A 183 MET cc_start: 0.9187 (tmm) cc_final: 0.8605 (tmm) REVERT: A 274 GLU cc_start: 0.8995 (pp20) cc_final: 0.8692 (pp20) REVERT: A 283 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8668 (tp30) REVERT: B 183 MET cc_start: 0.9072 (tmm) cc_final: 0.8804 (tmm) REVERT: B 184 MET cc_start: 0.9220 (tpp) cc_final: 0.8916 (tpp) REVERT: F 76 GLU cc_start: 0.8212 (pp20) cc_final: 0.7872 (pp20) REVERT: F 109 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 183 MET cc_start: 0.9177 (tmm) cc_final: 0.8416 (tmm) REVERT: F 206 ASN cc_start: 0.9082 (t0) cc_final: 0.8282 (m-40) REVERT: F 245 LYS cc_start: 0.9083 (mttp) cc_final: 0.8651 (mtmm) REVERT: F 251 LYS cc_start: 0.8152 (tptt) cc_final: 0.7540 (tptp) REVERT: F 254 ASN cc_start: 0.7265 (m110) cc_final: 0.6982 (m-40) REVERT: F 280 MET cc_start: 0.8701 (mmm) cc_final: 0.8306 (mmm) REVERT: G 171 ASP cc_start: 0.7879 (t0) cc_final: 0.7615 (t0) REVERT: G 183 MET cc_start: 0.8931 (tmm) cc_final: 0.8365 (tmm) REVERT: G 206 ASN cc_start: 0.8891 (t0) cc_final: 0.8450 (m-40) REVERT: G 255 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8233 (p) REVERT: G 274 GLU cc_start: 0.8961 (pp20) cc_final: 0.8606 (pp20) REVERT: G 280 MET cc_start: 0.8945 (mmm) cc_final: 0.8537 (mmm) REVERT: G 307 TRP cc_start: 0.9145 (m100) cc_final: 0.8312 (m100) REVERT: G 315 ILE cc_start: 0.6413 (OUTLIER) cc_final: 0.5842 (mt) REVERT: G 333 PHE cc_start: 0.8087 (m-10) cc_final: 0.7757 (m-80) outliers start: 34 outliers final: 28 residues processed: 142 average time/residue: 0.1683 time to fit residues: 37.0816 Evaluate side-chains 144 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 122 optimal weight: 0.0050 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10679 Z= 0.185 Angle : 0.638 10.246 14454 Z= 0.327 Chirality : 0.047 0.436 1639 Planarity : 0.004 0.042 1800 Dihedral : 16.243 155.325 1716 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.88 % Allowed : 29.71 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1324 helix: 0.24 (0.29), residues: 372 sheet: -0.28 (0.36), residues: 236 loop : -1.55 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 307 HIS 0.003 0.001 HIS F 176 PHE 0.014 0.001 PHE G 105 TYR 0.019 0.002 TYR B 281 ARG 0.002 0.000 ARG F 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.9491 (mt) cc_final: 0.9213 (tp) REVERT: A 183 MET cc_start: 0.9263 (tmm) cc_final: 0.8723 (tmm) REVERT: A 274 GLU cc_start: 0.8917 (pp20) cc_final: 0.8574 (pp20) REVERT: A 280 MET cc_start: 0.9072 (tpp) cc_final: 0.8790 (tpp) REVERT: A 283 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8659 (tp30) REVERT: B 40 MET cc_start: 0.8739 (ptp) cc_final: 0.8194 (ppp) REVERT: B 183 MET cc_start: 0.9100 (tmm) cc_final: 0.8812 (tmm) REVERT: B 184 MET cc_start: 0.9162 (tpp) cc_final: 0.8804 (tpp) REVERT: B 280 MET cc_start: 0.8259 (mmm) cc_final: 0.7400 (mmm) REVERT: F 69 TYR cc_start: 0.8940 (m-80) cc_final: 0.8709 (m-80) REVERT: F 76 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7884 (pp20) REVERT: F 183 MET cc_start: 0.9173 (tmm) cc_final: 0.8379 (tmm) REVERT: F 206 ASN cc_start: 0.9035 (t0) cc_final: 0.8236 (m-40) REVERT: F 212 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8295 (p) REVERT: F 251 LYS cc_start: 0.8076 (tptt) cc_final: 0.7500 (tptp) REVERT: F 274 GLU cc_start: 0.9047 (pp20) cc_final: 0.8756 (pm20) REVERT: F 280 MET cc_start: 0.8516 (mmm) cc_final: 0.8203 (mmm) REVERT: G 40 MET cc_start: 0.8777 (mtp) cc_final: 0.7551 (ttm) REVERT: G 183 MET cc_start: 0.8995 (tmm) cc_final: 0.8384 (tmm) REVERT: G 206 ASN cc_start: 0.8771 (t0) cc_final: 0.8461 (t0) REVERT: G 253 THR cc_start: 0.5951 (OUTLIER) cc_final: 0.5657 (m) REVERT: G 255 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8075 (p) REVERT: G 274 GLU cc_start: 0.8881 (pp20) cc_final: 0.8524 (pp20) REVERT: G 280 MET cc_start: 0.8766 (mmm) cc_final: 0.8318 (mmm) REVERT: G 307 TRP cc_start: 0.9146 (m100) cc_final: 0.8339 (m100) REVERT: G 315 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6072 (mt) REVERT: G 325 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7656 (p90) REVERT: G 333 PHE cc_start: 0.8037 (m-10) cc_final: 0.7709 (m-80) outliers start: 30 outliers final: 22 residues processed: 141 average time/residue: 0.1710 time to fit residues: 37.3183 Evaluate side-chains 142 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 TYR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 315 ILE Chi-restraints excluded: chain G residue 325 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 40.0000 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.118435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085732 restraints weight = 28256.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.088430 restraints weight = 14141.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.090156 restraints weight = 9382.248| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10679 Z= 0.307 Angle : 0.695 11.082 14454 Z= 0.358 Chirality : 0.048 0.398 1639 Planarity : 0.004 0.039 1800 Dihedral : 16.513 155.598 1716 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.56 % Allowed : 29.33 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1324 helix: 0.45 (0.29), residues: 368 sheet: -0.22 (0.36), residues: 236 loop : -1.63 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 307 HIS 0.003 0.001 HIS F 176 PHE 0.018 0.002 PHE G 105 TYR 0.026 0.002 TYR A 325 ARG 0.003 0.000 ARG F 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.30 seconds wall clock time: 32 minutes 34.68 seconds (1954.68 seconds total)