Starting phenix.real_space_refine on Fri Mar 15 02:26:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/03_2024/8amd_15524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/03_2024/8amd_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_15524/03_2024/8amd_15524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/03_2024/8amd_15524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/03_2024/8amd_15524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amd_15524/03_2024/8amd_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-dev-5265/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: 6.68, per 1000 atoms: 0.64 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: 4.44 Conformation dependent library (CDL) restraints added in 1.7 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: 2.08 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: 2.80 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: 1.21 - 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: 0.250 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: 0.000 Extract box with map and model: 1.950 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.930 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- 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 : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8819 (tp40) cc_final: 0.7900 (tp40) REVERT: A 107 ASP cc_start: 0.8351 (t0) cc_final: 0.7889 (t0) REVERT: A 167 GLU cc_start: 0.8904 (pp20) cc_final: 0.8253 (tm-30) REVERT: A 197 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8595 (tttt) REVERT: A 254 ASN cc_start: 0.8348 (m-40) cc_final: 0.7919 (p0) REVERT: B 18 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7175 (mm-30) REVERT: B 125 ASP cc_start: 0.8595 (p0) cc_final: 0.8314 (p0) REVERT: B 157 ASP cc_start: 0.7836 (p0) cc_final: 0.7572 (p0) REVERT: B 183 MET cc_start: 0.8670 (ttp) cc_final: 0.8434 (ttt) REVERT: F 157 ASP cc_start: 0.8084 (t0) cc_final: 0.7616 (t70) REVERT: F 183 MET cc_start: 0.8601 (ttp) cc_final: 0.8154 (tmm) REVERT: F 323 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8390 (ptpt) REVERT: F 325 TYR cc_start: 0.7929 (t80) cc_final: 0.7598 (t80) REVERT: G 41 ARG cc_start: 0.8103 (mpt-90) cc_final: 0.6637 (tmt170) REVERT: G 197 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8962 (ttmm) REVERT: G 205 ILE cc_start: 0.9193 (pt) cc_final: 0.8580 (pt) REVERT: G 211 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8715 (ttmm) REVERT: G 252 GLU cc_start: 0.7350 (mp0) cc_final: 0.5747 (pp20) outliers start: 9 outliers final: 4 residues processed: 220 average time/residue: 0.2170 time to fit residues: 66.8662 Evaluate side-chains 158 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 154 VAL 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 95 GLN A 137 GLN A 186 GLN A 196 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10532 Z= 0.361 Angle : 0.710 8.127 14232 Z= 0.381 Chirality : 0.047 0.202 1611 Planarity : 0.004 0.045 1796 Dihedral : 14.786 88.814 1608 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.42 % Allowed : 21.06 % Favored : 74.52 % 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: -4.39 (0.18), residues: 1324 helix: -3.14 (0.21), residues: 340 sheet: -2.72 (0.33), residues: 192 loop : -2.97 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 307 HIS 0.009 0.001 HIS B 329 PHE 0.018 0.002 PHE B 105 TYR 0.038 0.003 TYR B 78 ARG 0.004 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 208 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: A 95 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8340 (tp40) REVERT: A 107 ASP cc_start: 0.8316 (t0) cc_final: 0.8081 (t0) REVERT: A 167 GLU cc_start: 0.8928 (pp20) cc_final: 0.8434 (tm-30) REVERT: A 197 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8705 (tttt) REVERT: A 208 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 254 ASN cc_start: 0.8321 (m-40) cc_final: 0.7941 (p0) REVERT: B 18 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7156 (mm-30) REVERT: B 53 MET cc_start: 0.8377 (tmm) cc_final: 0.7201 (tmm) REVERT: B 76 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6400 (pm20) REVERT: B 125 ASP cc_start: 0.8644 (p0) cc_final: 0.8349 (p0) REVERT: B 183 MET cc_start: 0.8728 (ttp) cc_final: 0.8408 (ttt) REVERT: B 186 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: F 53 MET cc_start: 0.8876 (tmm) cc_final: 0.8020 (tmm) REVERT: F 280 MET cc_start: 0.8483 (mtt) cc_final: 0.8232 (mpp) REVERT: F 325 TYR cc_start: 0.8061 (t80) cc_final: 0.7675 (t80) REVERT: G 41 ARG cc_start: 0.8110 (mpt-90) cc_final: 0.6502 (tpt170) REVERT: G 76 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: G 183 MET cc_start: 0.8821 (ttp) cc_final: 0.8441 (tmm) REVERT: G 207 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8671 (mm-40) REVERT: G 215 MET cc_start: 0.7999 (pmm) cc_final: 0.7614 (pmm) outliers start: 46 outliers final: 32 residues processed: 196 average time/residue: 0.2015 time to fit residues: 57.2678 Evaluate side-chains 183 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 285 ILE 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: 5.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.0170 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7899 moved from start: 0.1808 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= 0.246 Angle : 0.626 8.462 14232 Z= 0.337 Chirality : 0.045 0.193 1611 Planarity : 0.004 0.044 1796 Dihedral : 14.562 89.368 1608 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.29 % Allowed : 21.92 % Favored : 72.79 % 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: -3.91 (0.19), residues: 1324 helix: -2.79 (0.24), residues: 320 sheet: -2.31 (0.35), residues: 192 loop : -2.69 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.005 0.001 HIS G 329 PHE 0.013 0.001 PHE B 105 TYR 0.033 0.003 TYR B 78 ARG 0.002 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 216 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: A 95 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8395 (tp40) REVERT: A 167 GLU cc_start: 0.9029 (pp20) cc_final: 0.8471 (tm-30) REVERT: A 197 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8623 (tttt) REVERT: A 254 ASN cc_start: 0.8280 (m-40) cc_final: 0.7969 (p0) REVERT: B 18 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7129 (mm-30) REVERT: B 53 MET cc_start: 0.8181 (tmm) cc_final: 0.7856 (tmm) REVERT: B 76 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6298 (pm20) REVERT: B 125 ASP cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: B 183 MET cc_start: 0.8655 (ttp) cc_final: 0.8406 (ttt) REVERT: B 258 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6520 (tm-30) REVERT: F 53 MET cc_start: 0.8950 (tmm) cc_final: 0.8076 (tmm) REVERT: F 272 PHE cc_start: 0.8283 (m-10) cc_final: 0.7896 (m-80) REVERT: F 280 MET cc_start: 0.8405 (mtt) cc_final: 0.8174 (mtt) REVERT: F 290 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8871 (tm-30) REVERT: F 325 TYR cc_start: 0.8043 (t80) cc_final: 0.7642 (t80) REVERT: G 41 ARG cc_start: 0.8014 (mpt-90) cc_final: 0.6401 (tpt170) REVERT: G 76 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: G 183 MET cc_start: 0.8722 (ttp) cc_final: 0.8387 (tmm) REVERT: G 207 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: G 215 MET cc_start: 0.7998 (pmm) cc_final: 0.7300 (pmm) REVERT: G 278 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7897 (mt-10) REVERT: G 310 TYR cc_start: 0.6890 (t80) cc_final: 0.6410 (t80) REVERT: G 325 TYR cc_start: 0.7828 (t80) cc_final: 0.7487 (t80) outliers start: 55 outliers final: 36 residues processed: 198 average time/residue: 0.1953 time to fit residues: 56.1358 Evaluate side-chains 192 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 57 optimal weight: 0.0870 chunk 81 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 63 optimal weight: 0.0070 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 40.0000 overall best weight: 2.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 196 ASN ** 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 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN G 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10532 Z= 0.197 Angle : 0.595 7.979 14232 Z= 0.318 Chirality : 0.044 0.190 1611 Planarity : 0.004 0.040 1796 Dihedral : 14.372 89.922 1608 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 6.35 % Allowed : 22.40 % Favored : 71.25 % 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: -3.45 (0.20), residues: 1324 helix: -2.26 (0.27), residues: 296 sheet: -2.02 (0.35), residues: 192 loop : -2.48 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 307 HIS 0.004 0.001 HIS G 329 PHE 0.013 0.001 PHE A 105 TYR 0.030 0.002 TYR B 78 ARG 0.002 0.000 ARG F 235 *********************** 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 231 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 165 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: A 95 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8378 (tp40) REVERT: A 167 GLU cc_start: 0.9001 (pp20) cc_final: 0.8480 (tm-30) REVERT: A 197 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8468 (tttt) REVERT: A 254 ASN cc_start: 0.8262 (m-40) cc_final: 0.7980 (p0) REVERT: B 18 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7253 (mm-30) REVERT: B 53 MET cc_start: 0.8101 (tmm) cc_final: 0.7103 (tmm) REVERT: B 76 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: B 78 TYR cc_start: 0.8219 (p90) cc_final: 0.8003 (p90) REVERT: B 125 ASP cc_start: 0.8640 (p0) cc_final: 0.8333 (p0) REVERT: B 157 ASP cc_start: 0.7435 (p0) cc_final: 0.7122 (p0) REVERT: B 183 MET cc_start: 0.8642 (ttp) cc_final: 0.8388 (ttt) REVERT: B 258 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6532 (tm-30) REVERT: F 53 MET cc_start: 0.9032 (tmm) cc_final: 0.8165 (tmm) REVERT: F 272 PHE cc_start: 0.8244 (m-10) cc_final: 0.7926 (m-80) REVERT: F 280 MET cc_start: 0.8446 (mtt) cc_final: 0.8154 (mtt) REVERT: F 325 TYR cc_start: 0.8001 (t80) cc_final: 0.7593 (t80) REVERT: G 41 ARG cc_start: 0.8023 (mpt-90) cc_final: 0.6499 (tmt170) REVERT: G 183 MET cc_start: 0.8727 (ttp) cc_final: 0.8401 (tmm) REVERT: G 207 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: G 215 MET cc_start: 0.8219 (pmm) cc_final: 0.7412 (pmm) REVERT: G 252 GLU cc_start: 0.7289 (mp0) cc_final: 0.6132 (pm20) REVERT: G 310 TYR cc_start: 0.6816 (t80) cc_final: 0.6485 (t80) REVERT: G 319 SER cc_start: 0.8266 (t) cc_final: 0.7772 (m) REVERT: G 325 TYR cc_start: 0.7882 (t80) cc_final: 0.7425 (t80) outliers start: 66 outliers final: 45 residues processed: 213 average time/residue: 0.1887 time to fit residues: 58.4808 Evaluate side-chains 202 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 154 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 285 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 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 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2201 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= 0.167 Angle : 0.572 7.556 14232 Z= 0.307 Chirality : 0.044 0.187 1611 Planarity : 0.003 0.037 1796 Dihedral : 14.186 88.635 1608 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.06 % Allowed : 23.08 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.20), residues: 1324 helix: -1.77 (0.27), residues: 320 sheet: -1.91 (0.35), residues: 196 loop : -2.55 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 307 HIS 0.003 0.001 HIS G 329 PHE 0.013 0.001 PHE A 105 TYR 0.030 0.002 TYR F 310 ARG 0.002 0.000 ARG A 165 *********************** 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 224 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: A 95 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8415 (tp40) REVERT: A 167 GLU cc_start: 0.8967 (pp20) cc_final: 0.8435 (tm-30) REVERT: A 197 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8400 (tttt) REVERT: A 211 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8121 (ptpp) REVERT: A 254 ASN cc_start: 0.8244 (m-40) cc_final: 0.7999 (p0) REVERT: B 53 MET cc_start: 0.8039 (tmm) cc_final: 0.7072 (tmm) REVERT: B 76 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: B 78 TYR cc_start: 0.8207 (p90) cc_final: 0.7961 (p90) REVERT: B 125 ASP cc_start: 0.8631 (p0) cc_final: 0.8323 (p0) REVERT: B 157 ASP cc_start: 0.7426 (p0) cc_final: 0.7225 (p0) REVERT: B 258 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6136 (tm-30) REVERT: F 53 MET cc_start: 0.9029 (tmm) cc_final: 0.8157 (tmm) REVERT: F 272 PHE cc_start: 0.8225 (m-10) cc_final: 0.7928 (m-80) REVERT: F 280 MET cc_start: 0.8390 (mtt) cc_final: 0.8154 (mtt) REVERT: F 325 TYR cc_start: 0.7873 (t80) cc_final: 0.7526 (t80) REVERT: G 41 ARG cc_start: 0.8008 (mpt-90) cc_final: 0.6489 (tmt170) REVERT: G 76 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: G 183 MET cc_start: 0.8711 (ttp) cc_final: 0.8415 (tmm) REVERT: G 207 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7732 (mm-40) REVERT: G 215 MET cc_start: 0.8218 (pmm) cc_final: 0.7358 (pmm) REVERT: G 252 GLU cc_start: 0.7112 (mp0) cc_final: 0.6087 (pm20) REVERT: G 310 TYR cc_start: 0.6970 (t80) cc_final: 0.6634 (t80) REVERT: G 319 SER cc_start: 0.8034 (t) cc_final: 0.7668 (m) REVERT: G 325 TYR cc_start: 0.7898 (t80) cc_final: 0.7425 (t80) outliers start: 63 outliers final: 48 residues processed: 206 average time/residue: 0.1897 time to fit residues: 57.7028 Evaluate side-chains 204 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 128 optimal weight: 0.0870 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2309 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= 0.253 Angle : 0.603 7.319 14232 Z= 0.319 Chirality : 0.044 0.186 1611 Planarity : 0.004 0.037 1796 Dihedral : 14.276 89.699 1608 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 6.54 % Allowed : 23.17 % Favored : 70.29 % 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: -3.24 (0.20), residues: 1324 helix: -1.70 (0.27), residues: 324 sheet: -1.86 (0.35), residues: 196 loop : -2.52 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 307 HIS 0.004 0.001 HIS B 329 PHE 0.011 0.001 PHE B 105 TYR 0.026 0.002 TYR B 78 ARG 0.003 0.000 ARG B 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 228 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 160 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: A 95 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8439 (tp40) REVERT: A 167 GLU cc_start: 0.8982 (pp20) cc_final: 0.8481 (tm-30) REVERT: A 197 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8406 (tttt) REVERT: A 208 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 211 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8051 (ptpp) REVERT: A 254 ASN cc_start: 0.8255 (m-40) cc_final: 0.8013 (p0) REVERT: B 53 MET cc_start: 0.8102 (tmm) cc_final: 0.7031 (tmm) REVERT: B 76 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: B 125 ASP cc_start: 0.8631 (p0) cc_final: 0.8337 (p0) REVERT: B 157 ASP cc_start: 0.7552 (p0) cc_final: 0.7314 (p0) REVERT: B 258 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6746 (tm-30) REVERT: F 53 MET cc_start: 0.9046 (tmm) cc_final: 0.8172 (tmm) REVERT: F 272 PHE cc_start: 0.8239 (m-10) cc_final: 0.7948 (m-80) REVERT: F 277 VAL cc_start: 0.8883 (t) cc_final: 0.8615 (p) REVERT: F 280 MET cc_start: 0.8386 (mtt) cc_final: 0.8114 (mtt) REVERT: F 325 TYR cc_start: 0.7947 (t80) cc_final: 0.7555 (t80) REVERT: G 41 ARG cc_start: 0.8019 (mpt-90) cc_final: 0.6496 (tmt170) REVERT: G 76 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: G 183 MET cc_start: 0.8690 (ttp) cc_final: 0.8445 (tmm) REVERT: G 207 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7642 (mm-40) REVERT: G 215 MET cc_start: 0.8236 (pmm) cc_final: 0.7301 (pmm) REVERT: G 252 GLU cc_start: 0.7123 (mp0) cc_final: 0.5456 (pp20) REVERT: G 310 TYR cc_start: 0.6871 (t80) cc_final: 0.6492 (t80) REVERT: G 319 SER cc_start: 0.8096 (t) cc_final: 0.7669 (m) REVERT: G 325 TYR cc_start: 0.8053 (t80) cc_final: 0.7553 (t80) outliers start: 68 outliers final: 55 residues processed: 209 average time/residue: 0.1908 time to fit residues: 58.8294 Evaluate side-chains 213 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 277 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.0470 chunk 59 optimal weight: 6.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 196 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** F 321 ASN G 137 GLN G 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10532 Z= 0.159 Angle : 0.562 7.609 14232 Z= 0.301 Chirality : 0.043 0.183 1611 Planarity : 0.003 0.038 1796 Dihedral : 14.078 88.884 1608 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.25 % Allowed : 24.04 % 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: -3.04 (0.20), residues: 1324 helix: -1.55 (0.27), residues: 324 sheet: -1.63 (0.36), residues: 196 loop : -2.43 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.015 0.001 PHE A 105 TYR 0.025 0.002 TYR F 310 ARG 0.002 0.000 ARG B 235 *********************** 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 229 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 164 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: A 95 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8373 (tp40) REVERT: A 107 ASP cc_start: 0.8069 (t0) cc_final: 0.7724 (t0) REVERT: A 167 GLU cc_start: 0.8944 (pp20) cc_final: 0.8465 (tm-30) REVERT: A 197 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8423 (tttt) REVERT: A 211 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8069 (ptpp) REVERT: A 254 ASN cc_start: 0.8222 (m-40) cc_final: 0.8011 (p0) REVERT: B 53 MET cc_start: 0.7990 (tmm) cc_final: 0.7005 (tmm) REVERT: B 76 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.5992 (pm20) REVERT: B 125 ASP cc_start: 0.8620 (p0) cc_final: 0.8268 (p0) REVERT: B 157 ASP cc_start: 0.7531 (p0) cc_final: 0.7279 (p0) REVERT: B 258 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6723 (tm-30) REVERT: F 53 MET cc_start: 0.9030 (tmm) cc_final: 0.8179 (tmm) REVERT: F 183 MET cc_start: 0.8707 (tmm) cc_final: 0.8304 (tmm) REVERT: F 272 PHE cc_start: 0.8195 (m-10) cc_final: 0.7840 (m-80) REVERT: F 277 VAL cc_start: 0.8800 (t) cc_final: 0.8460 (p) REVERT: F 280 MET cc_start: 0.8357 (mtt) cc_final: 0.8051 (mtm) REVERT: F 325 TYR cc_start: 0.7929 (t80) cc_final: 0.7523 (t80) REVERT: G 41 ARG cc_start: 0.8004 (mpt-90) cc_final: 0.6482 (tmt170) REVERT: G 76 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: G 183 MET cc_start: 0.8687 (ttp) cc_final: 0.8472 (tmm) REVERT: G 207 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7463 (mm-40) REVERT: G 215 MET cc_start: 0.8290 (pmm) cc_final: 0.7318 (pmm) REVERT: G 252 GLU cc_start: 0.6883 (mp0) cc_final: 0.5941 (pm20) REVERT: G 310 TYR cc_start: 0.6805 (t80) cc_final: 0.6400 (t80) REVERT: G 319 SER cc_start: 0.7923 (t) cc_final: 0.7515 (m) REVERT: G 325 TYR cc_start: 0.8012 (t80) cc_final: 0.7537 (t80) outliers start: 65 outliers final: 49 residues processed: 211 average time/residue: 0.1919 time to fit residues: 60.1652 Evaluate side-chains 206 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 11 optimal weight: 0.0010 chunk 100 optimal weight: 20.0000 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10532 Z= 0.186 Angle : 0.567 7.730 14232 Z= 0.302 Chirality : 0.044 0.182 1611 Planarity : 0.003 0.037 1796 Dihedral : 14.044 88.892 1608 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 6.35 % Allowed : 25.00 % Favored : 68.65 % 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: -2.96 (0.21), residues: 1324 helix: -1.45 (0.27), residues: 324 sheet: -1.57 (0.36), residues: 196 loop : -2.38 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.014 0.001 PHE A 105 TYR 0.022 0.002 TYR F 310 ARG 0.001 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 217 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: A 95 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8277 (tp40) REVERT: A 167 GLU cc_start: 0.8947 (pp20) cc_final: 0.8482 (tm-30) REVERT: A 197 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8434 (tttt) REVERT: A 211 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8074 (ptpp) REVERT: B 53 MET cc_start: 0.8024 (tmm) cc_final: 0.7056 (tmm) REVERT: B 76 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: B 125 ASP cc_start: 0.8616 (p0) cc_final: 0.8266 (p0) REVERT: B 157 ASP cc_start: 0.7536 (p0) cc_final: 0.7276 (p0) REVERT: B 255 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 258 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6729 (tm-30) REVERT: B 313 GLU cc_start: 0.1512 (OUTLIER) cc_final: 0.1271 (pp20) REVERT: F 53 MET cc_start: 0.9056 (tmm) cc_final: 0.8191 (tmm) REVERT: F 183 MET cc_start: 0.8723 (tmm) cc_final: 0.8320 (tmm) REVERT: F 272 PHE cc_start: 0.8177 (m-10) cc_final: 0.7901 (m-80) REVERT: F 277 VAL cc_start: 0.8815 (t) cc_final: 0.8475 (p) REVERT: F 280 MET cc_start: 0.8346 (mtt) cc_final: 0.8045 (mtm) REVERT: F 325 TYR cc_start: 0.7994 (t80) cc_final: 0.7576 (t80) REVERT: G 41 ARG cc_start: 0.7956 (mpt-90) cc_final: 0.6432 (tmt170) REVERT: G 207 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7520 (mm-40) REVERT: G 215 MET cc_start: 0.8330 (pmm) cc_final: 0.7504 (pmm) REVERT: G 252 GLU cc_start: 0.6809 (mp0) cc_final: 0.5408 (pp20) REVERT: G 310 TYR cc_start: 0.6616 (t80) cc_final: 0.6215 (t80) REVERT: G 319 SER cc_start: 0.7937 (t) cc_final: 0.7552 (m) REVERT: G 325 TYR cc_start: 0.8054 (t80) cc_final: 0.7562 (t80) outliers start: 66 outliers final: 53 residues processed: 199 average time/residue: 0.1962 time to fit residues: 57.6455 Evaluate side-chains 209 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 278 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 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 24 ASN ** 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** G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10532 Z= 0.343 Angle : 0.655 7.562 14232 Z= 0.344 Chirality : 0.046 0.183 1611 Planarity : 0.004 0.038 1796 Dihedral : 14.308 92.214 1608 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 6.35 % Allowed : 25.29 % Favored : 68.37 % 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: -3.05 (0.20), residues: 1324 helix: -1.55 (0.27), residues: 328 sheet: -1.73 (0.35), residues: 196 loop : -2.41 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.004 0.001 HIS B 329 PHE 0.013 0.002 PHE B 105 TYR 0.022 0.002 TYR F 310 ARG 0.003 0.000 ARG G 209 *********************** 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 216 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 150 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: A 95 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8269 (tp40) REVERT: A 153 LEU cc_start: 0.9285 (tp) cc_final: 0.8818 (tp) REVERT: A 167 GLU cc_start: 0.8996 (pp20) cc_final: 0.8549 (tm-30) REVERT: A 176 HIS cc_start: 0.8765 (m-70) cc_final: 0.7851 (m170) REVERT: A 197 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8482 (tttt) REVERT: A 211 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8120 (ptpp) REVERT: B 53 MET cc_start: 0.8158 (tmm) cc_final: 0.7145 (tmm) REVERT: B 76 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6163 (pm20) REVERT: B 125 ASP cc_start: 0.8621 (p0) cc_final: 0.8354 (p0) REVERT: B 258 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6614 (tm-30) REVERT: B 313 GLU cc_start: 0.1599 (OUTLIER) cc_final: 0.1311 (pp20) REVERT: F 53 MET cc_start: 0.9049 (tmm) cc_final: 0.8202 (tmm) REVERT: F 272 PHE cc_start: 0.8225 (m-10) cc_final: 0.7934 (m-80) REVERT: F 277 VAL cc_start: 0.8937 (t) cc_final: 0.8692 (p) REVERT: F 280 MET cc_start: 0.8365 (mtt) cc_final: 0.8100 (mtt) REVERT: F 325 TYR cc_start: 0.7970 (t80) cc_final: 0.7530 (t80) REVERT: G 41 ARG cc_start: 0.7978 (mpt-90) cc_final: 0.6481 (tmt170) REVERT: G 76 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: G 207 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: G 215 MET cc_start: 0.8253 (pmm) cc_final: 0.7353 (pmm) REVERT: G 252 GLU cc_start: 0.6982 (mp0) cc_final: 0.5388 (pp20) REVERT: G 310 TYR cc_start: 0.6708 (t80) cc_final: 0.6279 (t80) REVERT: G 319 SER cc_start: 0.7997 (t) cc_final: 0.7609 (m) REVERT: G 325 TYR cc_start: 0.8039 (t80) cc_final: 0.7691 (t80) outliers start: 66 outliers final: 54 residues processed: 200 average time/residue: 0.1892 time to fit residues: 55.5752 Evaluate side-chains 206 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 147 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 0.0470 chunk 121 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 83 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN F 24 ASN F 137 GLN F 241 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2721 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= 0.153 Angle : 0.580 8.055 14232 Z= 0.308 Chirality : 0.044 0.178 1611 Planarity : 0.003 0.040 1796 Dihedral : 13.970 89.886 1608 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.71 % Allowed : 26.92 % Favored : 68.37 % 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: -2.82 (0.21), residues: 1324 helix: -1.29 (0.28), residues: 324 sheet: -1.48 (0.35), residues: 196 loop : -2.31 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 307 HIS 0.003 0.001 HIS F 110 PHE 0.017 0.001 PHE A 105 TYR 0.041 0.002 TYR F 310 ARG 0.003 0.000 ARG G 189 ********************** 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 211 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7729 (tppt) REVERT: A 76 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 95 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8371 (tp40) REVERT: A 167 GLU cc_start: 0.8919 (pp20) cc_final: 0.8509 (tm-30) REVERT: A 197 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8406 (tttt) REVERT: A 211 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8071 (ptpp) REVERT: B 53 MET cc_start: 0.8057 (tmm) cc_final: 0.7073 (tmm) REVERT: B 76 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.5893 (pm20) REVERT: B 125 ASP cc_start: 0.8598 (p0) cc_final: 0.8304 (p0) REVERT: B 157 ASP cc_start: 0.7582 (p0) cc_final: 0.7323 (p0) REVERT: B 258 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 313 GLU cc_start: 0.1524 (OUTLIER) cc_final: 0.1318 (pp20) REVERT: F 53 MET cc_start: 0.9032 (tmm) cc_final: 0.8158 (tmm) REVERT: F 183 MET cc_start: 0.8630 (tmm) cc_final: 0.8245 (tmm) REVERT: F 272 PHE cc_start: 0.8173 (m-80) cc_final: 0.7899 (m-80) REVERT: F 277 VAL cc_start: 0.8749 (t) cc_final: 0.8381 (p) REVERT: F 280 MET cc_start: 0.8265 (mtt) cc_final: 0.7966 (mtm) REVERT: F 325 TYR cc_start: 0.7970 (t80) cc_final: 0.7542 (t80) REVERT: G 207 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7761 (mm-40) REVERT: G 215 MET cc_start: 0.8346 (pmm) cc_final: 0.7527 (pmm) REVERT: G 252 GLU cc_start: 0.6759 (mp0) cc_final: 0.5891 (pm20) REVERT: G 310 TYR cc_start: 0.6561 (t80) cc_final: 0.6071 (t80) REVERT: G 319 SER cc_start: 0.7968 (t) cc_final: 0.7632 (m) REVERT: G 325 TYR cc_start: 0.7862 (t80) cc_final: 0.7559 (t80) outliers start: 49 outliers final: 41 residues processed: 197 average time/residue: 0.1902 time to fit residues: 55.6512 Evaluate side-chains 198 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 210 GLU Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** G 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098438 restraints weight = 19549.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101743 restraints weight = 10549.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103966 restraints weight = 7103.158| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10532 Z= 0.226 Angle : 0.601 7.859 14232 Z= 0.318 Chirality : 0.044 0.180 1611 Planarity : 0.004 0.038 1796 Dihedral : 14.019 89.664 1608 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.90 % Allowed : 27.31 % Favored : 67.79 % 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: -2.76 (0.21), residues: 1324 helix: -1.33 (0.28), residues: 320 sheet: -1.44 (0.35), residues: 196 loop : -2.24 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 307 HIS 0.003 0.001 HIS B 329 PHE 0.012 0.001 PHE A 105 TYR 0.022 0.002 TYR B 325 ARG 0.002 0.000 ARG F 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.76 seconds wall clock time: 37 minutes 36.38 seconds (2256.38 seconds total)