Starting phenix.real_space_refine on Sat Dec 9 07:11:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/12_2023/8amd_15524_updated.pdb" } resolution = 3.9 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 23 5.49 5 S 32 5.16 5 C 6460 2.51 5 N 1772 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F ASP 312": "OD1" <-> "OD2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F ASP 337": "OD1" <-> "OD2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 125": "OD1" <-> "OD2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G ASP 299": "OD1" <-> "OD2" Residue "G ASP 312": "OD1" <-> "OD2" 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10377 Number of models: 1 Model: "" Number of chains: 9 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: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 237 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.56 Number of scatterers: 10377 At special positions: 0 Unit cell: (100.928, 130.112, 144.704, 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 23 15.00 O 2090 8.00 N 1772 7.00 C 6460 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.0 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 10 sheets defined 28.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 26 through 31 removed outlier: 5.393A pdb=" N GLU A 31 " --> pdb=" O LEU A 27 " (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 64 Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.850A pdb=" N ALA A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 removed outlier: 4.138A pdb=" N ALA A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.870A pdb=" N GLU A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 181 through 191 removed outlier: 4.677A pdb=" N GLN A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.811A 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 296 removed outlier: 3.627A pdb=" N LEU A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 294 " --> pdb=" O GLU A 290 " (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 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 26 through 31 removed outlier: 5.389A pdb=" N GLU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' 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 64 Processing helix chain 'B' and resid 85 through 98 removed outlier: 4.015A pdb=" N ALA B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 removed outlier: 4.066A pdb=" N ALA B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 removed outlier: 4.090A pdb=" N GLU B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 181 through 191 removed outlier: 4.342A pdb=" N GLN B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.765A pdb=" N TYR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' 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 297 removed outlier: 3.681A pdb=" N LEU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.715A pdb=" N LYS B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 removed outlier: 4.746A pdb=" N ALA F 26 " --> pdb=" O ALA F 22 " (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 Processing helix chain 'F' and resid 85 through 98 removed outlier: 3.855A pdb=" N ALA F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 120 removed outlier: 4.170A pdb=" N ALA F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 removed outlier: 3.530A pdb=" N GLU F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 181 through 191 removed outlier: 4.618A pdb=" N GLN F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.648A 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 296 removed outlier: 3.768A pdb=" N LEU F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 294 " --> pdb=" O GLU F 290 " (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 334 through 337 No H-bonds generated for 'chain 'F' and resid 334 through 337' Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 26 through 31 removed outlier: 5.586A pdb=" N GLU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 85 through 98 removed outlier: 3.958A pdb=" N ALA G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 120 removed outlier: 4.186A pdb=" N ALA G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 148 removed outlier: 3.548A pdb=" N GLU G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 181 through 191 removed outlier: 4.316A pdb=" N GLN G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 231 removed outlier: 3.994A 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: 3.551A pdb=" N LEU G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) 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 260 through 265 removed outlier: 3.684A pdb=" N VAL A 264 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 235 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 234 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA A 202 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE A 77 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 204 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 205 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 155 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 157 " --> pdb=" O ILE A 106 " (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 277 through 280 removed outlier: 3.635A pdb=" N VAL A 255 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 244 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS A 257 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR A 242 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 275 through 280 removed outlier: 3.548A pdb=" N ILE B 261 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 277 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 234 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 238 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 202 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE B 77 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 204 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 203 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 242 through 248 removed outlier: 3.853A pdb=" N THR B 242 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY B 246 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLY B 248 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.619A 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: 3.979A pdb=" N VAL F 277 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 235 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 234 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA F 202 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE F 77 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE F 204 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLY F 79 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 155 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 242 through 248 removed outlier: 3.879A pdb=" N THR F 242 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY F 246 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN F 254 " --> pdb=" O GLY F 246 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY F 248 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU F 252 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 75 through 78 removed outlier: 6.397A pdb=" N VAL G 234 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR G 78 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 236 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS G 265 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASP G 237 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL G 263 " --> pdb=" O ASP G 237 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ARG G 239 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE G 261 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR G 259 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 277 " --> pdb=" O THR G 259 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 103 through 106 removed outlier: 7.168A pdb=" N LEU G 153 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE G 106 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE G 201 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL G 156 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE G 203 " --> pdb=" O VAL G 156 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'G' and resid 242 through 248 removed outlier: 3.880A pdb=" N THR G 242 " --> pdb=" O GLU G 258 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY G 246 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN G 254 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY G 248 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 3471 1.35 - 1.50: 2642 1.50 - 1.65: 4359 1.65 - 1.80: 43 1.80 - 1.94: 17 Bond restraints: 10532 Sorted by residual: bond pdb=" N GLN G 250 " pdb=" CA GLN G 250 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.57e+00 bond pdb=" N GLU G 331 " pdb=" CA GLU G 331 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.15e-02 7.56e+03 3.08e+00 bond pdb=" CB GLN F 250 " pdb=" CG GLN F 250 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" CA HIS G 329 " pdb=" CB HIS G 329 " ideal model delta sigma weight residual 1.533 1.565 -0.032 1.99e-02 2.53e+03 2.57e+00 bond pdb=" N GLU A 313 " pdb=" CA GLU A 313 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.58e-02 4.01e+03 2.52e+00 ... (remaining 10527 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 268 106.02 - 113.00: 5617 113.00 - 119.99: 3857 119.99 - 126.97: 4403 126.97 - 133.96: 87 Bond angle restraints: 14232 Sorted by residual: angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 113.10 106.21 6.89 9.70e-01 1.06e+00 5.04e+01 angle pdb=" N ILE F 332 " pdb=" CA ILE F 332 " pdb=" C ILE F 332 " ideal model delta sigma weight residual 112.90 106.45 6.45 9.60e-01 1.09e+00 4.51e+01 angle pdb=" N ILE G 332 " pdb=" CA ILE G 332 " pdb=" C ILE G 332 " ideal model delta sigma weight residual 113.22 106.23 6.99 1.23e+00 6.61e-01 3.23e+01 angle pdb=" N VAL F 255 " pdb=" CA VAL F 255 " pdb=" C VAL F 255 " ideal model delta sigma weight residual 113.20 108.45 4.75 9.60e-01 1.09e+00 2.45e+01 angle pdb=" N GLY F 217 " pdb=" CA GLY F 217 " pdb=" C GLY F 217 " ideal model delta sigma weight residual 110.77 118.97 -8.20 1.93e+00 2.68e-01 1.80e+01 ... (remaining 14227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5501 17.86 - 35.73: 673 35.73 - 53.59: 186 53.59 - 71.46: 52 71.46 - 89.32: 16 Dihedral angle restraints: 6428 sinusoidal: 2692 harmonic: 3736 Sorted by residual: dihedral pdb=" CA LYS F 314 " pdb=" C LYS F 314 " pdb=" N ILE F 315 " pdb=" CA ILE F 315 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA LYS G 314 " pdb=" C LYS G 314 " pdb=" N ILE G 315 " pdb=" CA ILE G 315 " ideal model delta harmonic sigma weight residual 180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ASP A 312 " pdb=" C ASP A 312 " pdb=" N GLU A 313 " pdb=" CA GLU A 313 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 6425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1124 0.053 - 0.106: 356 0.106 - 0.159: 106 0.159 - 0.211: 17 0.211 - 0.264: 8 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE G 285 " pdb=" CA ILE G 285 " pdb=" CG1 ILE G 285 " pdb=" CG2 ILE G 285 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA GLU G 313 " pdb=" N GLU G 313 " pdb=" C GLU G 313 " pdb=" CB GLU G 313 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1608 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 312 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C ASP G 312 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP G 312 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU G 313 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 312 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C ASP A 312 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP A 312 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C ASP B 312 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 312 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU B 313 " -0.015 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3191 2.82 - 3.34: 9185 3.34 - 3.86: 16088 3.86 - 4.38: 17260 4.38 - 4.90: 28877 Nonbonded interactions: 74601 Sorted by model distance: nonbonded pdb=" O PHE F 34 " pdb=" OG SER F 38 " model vdw 2.298 2.440 nonbonded pdb=" O1A AGS G 500 " pdb=" O2G AGS G 500 " model vdw 2.298 2.440 nonbonded pdb=" OD1 ASP B 147 " pdb=" OG SER B 194 " model vdw 2.317 2.440 nonbonded pdb=" O PHE B 34 " pdb=" OG SER B 38 " model vdw 2.325 2.440 nonbonded pdb=" N SER B 83 " pdb=" O1B AGS B 500 " model vdw 2.329 2.496 ... (remaining 74596 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: 0.260 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: 1.940 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 30.090 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10532 Z= 0.400 Angle : 0.963 11.264 14232 Z= 0.552 Chirality : 0.059 0.264 1611 Planarity : 0.006 0.058 1796 Dihedral : 17.828 89.319 4052 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 0.87 % Allowed : 14.33 % Favored : 84.81 % 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: -5.17 (0.16), residues: 1324 helix: -4.23 (0.14), residues: 340 sheet: -3.36 (0.30), residues: 196 loop : -3.18 (0.16), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 307 HIS 0.008 0.002 HIS F 329 PHE 0.020 0.002 PHE B 34 TYR 0.031 0.004 TYR G 116 ARG 0.004 0.001 ARG F 209 *********************** 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 221 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 212 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 220 average time/residue: 0.2263 time to fit residues: 69.4276 Evaluate side-chains 147 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0868 time to fit residues: 2.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 186 GLN A 196 ASN A 317 GLN B 91 HIS B 137 GLN B 196 ASN B 207 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN F 137 GLN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 196 ASN G 207 GLN G 317 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10532 Z= 0.363 Angle : 0.721 8.226 14232 Z= 0.386 Chirality : 0.047 0.200 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.757 88.758 1604 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.42 % Allowed : 20.67 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.18), residues: 1324 helix: -3.19 (0.22), residues: 316 sheet: -2.69 (0.33), residues: 192 loop : -2.77 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 307 HIS 0.005 0.002 HIS B 329 PHE 0.016 0.002 PHE B 105 TYR 0.037 0.003 TYR B 78 ARG 0.005 0.000 ARG F 235 *********************** 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 197 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.242 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 31 residues processed: 185 average time/residue: 0.1955 time to fit residues: 53.1423 Evaluate side-chains 168 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1100 time to fit residues: 7.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 82 optimal weight: 0.0270 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 207 GLN G 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10532 Z= 0.159 Angle : 0.610 8.557 14232 Z= 0.327 Chirality : 0.044 0.191 1611 Planarity : 0.004 0.040 1796 Dihedral : 14.276 87.195 1604 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.50 % Allowed : 22.88 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.19), residues: 1324 helix: -2.30 (0.25), residues: 320 sheet: -2.22 (0.35), residues: 192 loop : -2.71 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS G 329 PHE 0.014 0.001 PHE F 105 TYR 0.030 0.002 TYR B 78 ARG 0.001 0.000 ARG F 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 196 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 186 average time/residue: 0.2070 time to fit residues: 55.6376 Evaluate side-chains 161 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1007 time to fit residues: 3.7138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 63 optimal weight: 0.0170 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 40.0000 overall best weight: 3.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10532 Z= 0.256 Angle : 0.637 8.418 14232 Z= 0.336 Chirality : 0.045 0.191 1611 Planarity : 0.004 0.042 1796 Dihedral : 14.328 89.232 1604 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 3.17 % Allowed : 24.71 % Favored : 72.12 % 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: -3.41 (0.20), residues: 1324 helix: -2.21 (0.27), residues: 296 sheet: -2.15 (0.35), residues: 196 loop : -2.41 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 307 HIS 0.007 0.001 HIS G 329 PHE 0.022 0.002 PHE F 272 TYR 0.024 0.002 TYR A 78 ARG 0.003 0.000 ARG A 165 *********************** 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 190 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.319 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 176 average time/residue: 0.2050 time to fit residues: 53.0027 Evaluate side-chains 167 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1164 time to fit residues: 5.6096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 196 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10532 Z= 0.251 Angle : 0.634 8.899 14232 Z= 0.332 Chirality : 0.045 0.187 1611 Planarity : 0.004 0.045 1796 Dihedral : 14.349 90.482 1604 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.40 % Allowed : 26.54 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.20), residues: 1324 helix: -1.77 (0.27), residues: 320 sheet: -2.02 (0.34), residues: 196 loop : -2.53 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 307 HIS 0.008 0.001 HIS G 329 PHE 0.011 0.001 PHE B 105 TYR 0.034 0.002 TYR F 310 ARG 0.003 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 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.357 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 172 average time/residue: 0.1972 time to fit residues: 50.2875 Evaluate side-chains 158 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0976 time to fit residues: 4.3294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.4980 chunk 115 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 40.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10532 Z= 0.185 Angle : 0.594 8.793 14232 Z= 0.313 Chirality : 0.044 0.184 1611 Planarity : 0.004 0.046 1796 Dihedral : 14.151 89.766 1604 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.63 % Allowed : 27.31 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1324 helix: -1.62 (0.27), residues: 324 sheet: -1.78 (0.35), residues: 196 loop : -2.45 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 307 HIS 0.005 0.001 HIS G 329 PHE 0.017 0.001 PHE F 272 TYR 0.020 0.002 TYR A 78 ARG 0.002 0.000 ARG A 19 *********************** 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 172 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.222 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 162 average time/residue: 0.2210 time to fit residues: 52.2072 Evaluate side-chains 156 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0935 time to fit residues: 3.4540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10532 Z= 0.263 Angle : 0.641 8.894 14232 Z= 0.334 Chirality : 0.045 0.183 1611 Planarity : 0.004 0.045 1796 Dihedral : 14.240 91.236 1604 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.12 % Allowed : 27.98 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1324 helix: -1.50 (0.28), residues: 324 sheet: -1.79 (0.35), residues: 196 loop : -2.42 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 307 HIS 0.011 0.001 HIS F 329 PHE 0.012 0.001 PHE A 105 TYR 0.023 0.002 TYR F 310 ARG 0.005 0.000 ARG G 165 *********************** 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 169 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.2083 time to fit residues: 49.1919 Evaluate side-chains 156 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1172 time to fit residues: 4.4968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10532 Z= 0.251 Angle : 0.635 8.762 14232 Z= 0.334 Chirality : 0.045 0.181 1611 Planarity : 0.004 0.047 1796 Dihedral : 14.230 91.728 1604 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.25 % Allowed : 28.65 % Favored : 70.10 % 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: -2.97 (0.21), residues: 1324 helix: -1.49 (0.27), residues: 324 sheet: -1.74 (0.35), residues: 196 loop : -2.33 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.008 0.001 HIS A 176 PHE 0.016 0.001 PHE F 272 TYR 0.021 0.002 TYR A 78 ARG 0.004 0.000 ARG G 165 *********************** 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 155 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.204 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 153 average time/residue: 0.2153 time to fit residues: 48.2865 Evaluate side-chains 145 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0984 time to fit residues: 2.4336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 126 optimal weight: 0.0070 overall best weight: 2.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10532 Z= 0.206 Angle : 0.614 9.036 14232 Z= 0.322 Chirality : 0.044 0.181 1611 Planarity : 0.004 0.046 1796 Dihedral : 14.098 91.151 1604 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.96 % Allowed : 29.33 % Favored : 69.71 % 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: -2.86 (0.21), residues: 1324 helix: -1.37 (0.28), residues: 320 sheet: -1.58 (0.35), residues: 196 loop : -2.30 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.016 0.001 PHE A 105 TYR 0.046 0.002 TYR F 310 ARG 0.004 0.000 ARG G 165 *********************** 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 165 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 161 average time/residue: 0.2018 time to fit residues: 47.5900 Evaluate side-chains 152 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1024 time to fit residues: 2.9709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 0.0060 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.0020 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10532 Z= 0.167 Angle : 0.609 8.843 14232 Z= 0.320 Chirality : 0.044 0.177 1611 Planarity : 0.003 0.045 1796 Dihedral : 13.902 89.816 1604 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.29 % Allowed : 30.19 % Favored : 69.52 % 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: -2.73 (0.21), residues: 1324 helix: -1.28 (0.28), residues: 320 sheet: -1.38 (0.36), residues: 196 loop : -2.24 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 307 HIS 0.004 0.001 HIS B 176 PHE 0.017 0.001 PHE F 272 TYR 0.039 0.002 TYR F 310 ARG 0.003 0.000 ARG G 165 ********************** 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 156 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 154 average time/residue: 0.2111 time to fit residues: 47.4836 Evaluate side-chains 141 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1079 time to fit residues: 2.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 105 optimal weight: 0.1980 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099914 restraints weight = 19543.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103162 restraints weight = 10813.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105341 restraints weight = 7395.837| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10532 Z= 0.222 Angle : 0.632 8.765 14232 Z= 0.331 Chirality : 0.044 0.179 1611 Planarity : 0.004 0.038 1796 Dihedral : 13.962 90.814 1604 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.29 % Allowed : 30.67 % Favored : 69.04 % 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: -2.78 (0.21), residues: 1324 helix: -1.43 (0.27), residues: 340 sheet: -1.32 (0.36), residues: 196 loop : -2.26 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 307 HIS 0.003 0.001 HIS G 329 PHE 0.012 0.001 PHE A 105 TYR 0.038 0.002 TYR F 310 ARG 0.003 0.000 ARG G 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.75 seconds wall clock time: 37 minutes 23.58 seconds (2243.58 seconds total)