Starting phenix.real_space_refine on Wed Apr 10 07:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8own_17240/04_2024/8own_17240.pdb" } resolution = 3.26 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= 0.007 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 Ca 6 9.91 5 S 96 5.16 5 C 11844 2.51 5 N 3330 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F GLU 309": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18804 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "B" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "C" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "E" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "F" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.37, per 1000 atoms: 0.55 Number of scatterers: 18804 At special positions: 0 Unit cell: (116.96, 116.1, 124.7, 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) Ca 6 19.99 S 96 16.00 O 3528 8.00 N 3330 7.00 C 11844 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=0, symmetry=0 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.7 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 9 sheets defined 57.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.704A pdb=" N ALA A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE A 132 " --> pdb=" O HIS A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.867A pdb=" N ASN A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 358 through 385 Processing helix chain 'A' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 76 through 95 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE B 132 " --> pdb=" O HIS B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 132' Processing helix chain 'B' and resid 146 through 162 removed outlier: 3.562A pdb=" N MET B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 358 through 385 Processing helix chain 'B' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 removed outlier: 4.391A pdb=" N THR C 7 " --> pdb=" O ALA C 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 76 through 95 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE C 132 " --> pdb=" O HIS C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 146 through 162 removed outlier: 3.564A pdb=" N MET C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.835A pdb=" N TYR C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 354 Processing helix chain 'C' and resid 358 through 385 Processing helix chain 'C' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 76 through 95 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE D 132 " --> pdb=" O HIS D 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 132' Processing helix chain 'D' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 removed outlier: 4.257A pdb=" N VAL D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 327 Processing helix chain 'D' and resid 332 through 337 removed outlier: 3.867A pdb=" N ASN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 354 Processing helix chain 'D' and resid 358 through 385 Processing helix chain 'D' and resid 387 through 408 removed outlier: 3.584A pdb=" N GLY D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR E 7 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 Processing helix chain 'E' and resid 76 through 95 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE E 132 " --> pdb=" O HIS E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 132' Processing helix chain 'E' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL E 168 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.837A pdb=" N TYR E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 229 Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.835A pdb=" N LYS E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 327 Processing helix chain 'E' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'E' and resid 358 through 385 Processing helix chain 'E' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR F 7 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 Processing helix chain 'F' and resid 76 through 95 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 129 through 132 removed outlier: 3.842A pdb=" N ILE F 132 " --> pdb=" O HIS F 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 129 through 132' Processing helix chain 'F' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 removed outlier: 4.258A pdb=" N VAL F 168 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS F 255 " --> pdb=" O ASN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 295 through 300 removed outlier: 4.115A pdb=" N GLY F 300 " --> pdb=" O LYS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 327 Processing helix chain 'F' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN F 337 " --> pdb=" O ASP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 354 Processing helix chain 'F' and resid 358 through 385 Processing helix chain 'F' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY F 408 " --> pdb=" O THR F 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 141 removed outlier: 6.691A pdb=" N MET A 65 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA A 140 " --> pdb=" O MET A 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 67 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS A 66 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY A 103 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY A 68 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 105 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG A 70 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 100 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY D 100 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS D 66 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY D 103 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY D 68 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE D 105 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG D 70 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET D 65 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA D 140 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY D 67 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE A 209 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 235 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 211 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 208 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 286 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 210 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 307 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.692A pdb=" N MET B 65 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA B 140 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY B 67 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 66 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY B 103 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY B 68 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE B 105 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG B 70 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY B 100 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY E 100 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS E 66 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY E 103 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY E 68 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE E 105 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 70 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET E 65 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA E 140 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY E 67 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE B 209 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 235 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE B 211 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 208 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 286 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 210 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 307 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.691A pdb=" N MET C 65 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA C 140 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY C 67 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS C 66 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY C 103 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY C 68 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE C 105 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 70 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY C 100 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY F 100 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS F 66 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY F 103 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLY F 68 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE F 105 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG F 70 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET F 65 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA F 140 " --> pdb=" O MET F 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY F 67 " --> pdb=" O ALA F 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE C 209 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 235 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE C 211 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C 208 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 286 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 210 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 307 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE D 209 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 235 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 211 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR D 208 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE D 286 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 210 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE D 307 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE E 209 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 235 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E 211 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR E 208 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE E 286 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 210 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 307 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE F 209 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 235 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 211 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR F 208 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE F 286 " --> pdb=" O THR F 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 210 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 307 " --> pdb=" O LEU F 331 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3132 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: 6.30 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6365 1.34 - 1.45: 2297 1.45 - 1.57: 10358 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 19176 Sorted by residual: bond pdb=" CB THR E 91 " pdb=" CG2 THR E 91 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 bond pdb=" CB THR D 91 " pdb=" CG2 THR D 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CB THR F 91 " pdb=" CG2 THR F 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.89e-01 bond pdb=" CB THR B 91 " pdb=" CG2 THR B 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.84e-01 bond pdb=" CB THR C 91 " pdb=" CG2 THR C 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.78e-01 ... (remaining 19171 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.58: 536 106.58 - 113.48: 10651 113.48 - 120.37: 7311 120.37 - 127.27: 7230 127.27 - 134.17: 246 Bond angle restraints: 25974 Sorted by residual: angle pdb=" CA GLY E 215 " pdb=" C GLY E 215 " pdb=" O GLY E 215 " ideal model delta sigma weight residual 122.76 119.55 3.21 1.12e+00 7.97e-01 8.21e+00 angle pdb=" CA GLY A 215 " pdb=" C GLY A 215 " pdb=" O GLY A 215 " ideal model delta sigma weight residual 122.76 119.57 3.19 1.12e+00 7.97e-01 8.12e+00 angle pdb=" CA GLY C 215 " pdb=" C GLY C 215 " pdb=" O GLY C 215 " ideal model delta sigma weight residual 122.76 119.62 3.14 1.12e+00 7.97e-01 7.88e+00 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.76 119.64 3.12 1.12e+00 7.97e-01 7.76e+00 angle pdb=" CA GLY F 215 " pdb=" C GLY F 215 " pdb=" O GLY F 215 " ideal model delta sigma weight residual 122.76 119.65 3.11 1.12e+00 7.97e-01 7.70e+00 ... (remaining 25969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 10116 17.47 - 34.95: 1110 34.95 - 52.42: 132 52.42 - 69.90: 12 69.90 - 87.37: 24 Dihedral angle restraints: 11394 sinusoidal: 4476 harmonic: 6918 Sorted by residual: dihedral pdb=" CA PHE A 214 " pdb=" C PHE A 214 " pdb=" N GLY A 215 " pdb=" CA GLY A 215 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE F 214 " pdb=" C PHE F 214 " pdb=" N GLY F 215 " pdb=" CA GLY F 215 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE E 214 " pdb=" C PHE E 214 " pdb=" N GLY E 215 " pdb=" CA GLY E 215 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 11391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1497 0.026 - 0.053: 869 0.053 - 0.079: 326 0.079 - 0.105: 97 0.105 - 0.132: 115 Chirality restraints: 2904 Sorted by residual: chirality pdb=" CA ILE D 69 " pdb=" N ILE D 69 " pdb=" C ILE D 69 " pdb=" CB ILE D 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE E 69 " pdb=" N ILE E 69 " pdb=" C ILE E 69 " pdb=" CB ILE E 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2901 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 11 " -0.015 2.00e-02 2.50e+03 1.54e-02 4.16e+00 pdb=" CG PHE E 11 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 11 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE E 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 11 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 11 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE E 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 11 " 0.015 2.00e-02 2.50e+03 1.53e-02 4.10e+00 pdb=" CG PHE F 11 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 11 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 11 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 11 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 11 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 11 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 11 " -0.015 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE D 11 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 11 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 11 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 11 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 11 " 0.002 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5742 2.83 - 3.35: 17129 3.35 - 3.86: 29900 3.86 - 4.38: 33083 4.38 - 4.90: 61723 Nonbonded interactions: 147577 Sorted by model distance: nonbonded pdb=" NZ LYS D 102 " pdb=" OD2 ASP D 142 " model vdw 2.309 2.520 nonbonded pdb=" NZ LYS F 102 " pdb=" OD2 ASP F 142 " model vdw 2.310 2.520 nonbonded pdb=" NZ LYS C 102 " pdb=" OD2 ASP C 142 " model vdw 2.310 2.520 nonbonded pdb=" NZ LYS E 102 " pdb=" OD2 ASP E 142 " model vdw 2.310 2.520 nonbonded pdb=" NZ LYS B 102 " pdb=" OD2 ASP B 142 " model vdw 2.310 2.520 ... (remaining 147572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.020 Extract box with map and model: 10.990 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 50.300 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.005 0.030 19176 Z= 0.326 Angle : 0.590 8.077 25974 Z= 0.330 Chirality : 0.043 0.132 2904 Planarity : 0.004 0.045 3396 Dihedral : 14.021 87.372 6978 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: 0.78 (0.17), residues: 2448 helix: 2.30 (0.14), residues: 1212 sheet: -0.34 (0.27), residues: 426 loop : -1.86 (0.17), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 348 HIS 0.003 0.001 HIS D 129 PHE 0.035 0.003 PHE E 11 TYR 0.008 0.001 TYR E 51 ARG 0.005 0.001 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.211 Fit side-chains REVERT: A 303 LYS cc_start: 0.6542 (ptpt) cc_final: 0.5956 (pttt) REVERT: B 87 MET cc_start: 0.8861 (tpp) cc_final: 0.8617 (tpp) REVERT: B 303 LYS cc_start: 0.6756 (ptpt) cc_final: 0.6167 (pttt) REVERT: C 303 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6144 (pttt) REVERT: D 150 MET cc_start: 0.8667 (mmp) cc_final: 0.8449 (mmt) REVERT: D 238 ILE cc_start: 0.7859 (tp) cc_final: 0.7602 (mp) REVERT: D 256 HIS cc_start: 0.7066 (t-170) cc_final: 0.6818 (t-170) REVERT: E 65 MET cc_start: 0.8929 (mtt) cc_final: 0.8703 (mtt) REVERT: E 212 GLN cc_start: 0.7639 (tt0) cc_final: 0.7296 (tt0) REVERT: E 278 LEU cc_start: 0.7243 (mt) cc_final: 0.6940 (tt) REVERT: F 212 GLN cc_start: 0.7762 (tt0) cc_final: 0.7497 (tt0) REVERT: F 243 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6198 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3931 time to fit residues: 140.6842 Evaluate side-chains 171 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.7980 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN B 85 GLN C 85 GLN D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19176 Z= 0.302 Angle : 0.532 4.928 25974 Z= 0.286 Chirality : 0.043 0.156 2904 Planarity : 0.004 0.038 3396 Dihedral : 4.059 17.157 2616 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.27 % Allowed : 7.40 % Favored : 91.34 % 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: 0.89 (0.16), residues: 2448 helix: 2.28 (0.14), residues: 1230 sheet: -0.60 (0.33), residues: 276 loop : -1.40 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 348 HIS 0.004 0.001 HIS B 384 PHE 0.024 0.002 PHE A 11 TYR 0.013 0.001 TYR A 51 ARG 0.005 0.001 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 2.673 Fit side-chains REVERT: A 303 LYS cc_start: 0.7099 (ptpt) cc_final: 0.6228 (pttt) REVERT: B 87 MET cc_start: 0.8993 (tpp) cc_final: 0.8707 (tpp) REVERT: B 303 LYS cc_start: 0.6977 (ptpt) cc_final: 0.6273 (pttt) REVERT: C 303 LYS cc_start: 0.7168 (ptpt) cc_final: 0.6117 (pttt) REVERT: C 381 CYS cc_start: 0.7824 (t) cc_final: 0.7034 (m) REVERT: F 238 ILE cc_start: 0.7786 (tp) cc_final: 0.7537 (mp) outliers start: 25 outliers final: 17 residues processed: 190 average time/residue: 0.3543 time to fit residues: 99.8715 Evaluate side-chains 181 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 0.4980 chunk 152 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 405 GLN D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19176 Z= 0.192 Angle : 0.443 4.109 25974 Z= 0.240 Chirality : 0.040 0.134 2904 Planarity : 0.004 0.033 3396 Dihedral : 3.685 16.859 2616 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.17 % Allowed : 11.04 % Favored : 87.79 % 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: 1.32 (0.17), residues: 2448 helix: 2.67 (0.14), residues: 1230 sheet: -0.31 (0.31), residues: 342 loop : -1.33 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 348 HIS 0.004 0.001 HIS F 256 PHE 0.012 0.001 PHE B 11 TYR 0.011 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 2.127 Fit side-chains REVERT: A 303 LYS cc_start: 0.7057 (ptpt) cc_final: 0.6394 (pttt) REVERT: B 87 MET cc_start: 0.8902 (tpp) cc_final: 0.8674 (tpp) REVERT: B 281 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6227 (mm-30) REVERT: B 303 LYS cc_start: 0.7076 (ptpt) cc_final: 0.6339 (pttt) REVERT: B 321 GLU cc_start: 0.6591 (pt0) cc_final: 0.6326 (mt-10) REVERT: C 214 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7574 (m-10) REVERT: C 281 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6254 (mm-30) REVERT: C 303 LYS cc_start: 0.7207 (ptpt) cc_final: 0.6156 (pttt) REVERT: C 381 CYS cc_start: 0.7792 (t) cc_final: 0.6984 (m) outliers start: 23 outliers final: 19 residues processed: 195 average time/residue: 0.3361 time to fit residues: 98.2945 Evaluate side-chains 184 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS B 280 HIS D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 19176 Z= 0.372 Angle : 0.538 4.920 25974 Z= 0.291 Chirality : 0.043 0.139 2904 Planarity : 0.004 0.039 3396 Dihedral : 4.034 15.221 2616 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.48 % Allowed : 11.60 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2448 helix: 2.46 (0.14), residues: 1224 sheet: -0.14 (0.32), residues: 324 loop : -1.54 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 348 HIS 0.006 0.001 HIS A 384 PHE 0.017 0.002 PHE A 374 TYR 0.012 0.001 TYR A 51 ARG 0.005 0.001 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 2.184 Fit side-chains REVERT: A 117 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 303 LYS cc_start: 0.7063 (ptpt) cc_final: 0.6222 (pttt) REVERT: B 87 MET cc_start: 0.9011 (tpp) cc_final: 0.8676 (tpp) REVERT: B 214 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7659 (m-10) REVERT: B 303 LYS cc_start: 0.7005 (ptpt) cc_final: 0.6426 (pttt) REVERT: C 214 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: C 303 LYS cc_start: 0.7048 (ptpt) cc_final: 0.6168 (pttt) REVERT: C 381 CYS cc_start: 0.7851 (t) cc_final: 0.6998 (m) REVERT: D 410 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: F 272 MET cc_start: 0.6606 (tpt) cc_final: 0.5932 (mmt) outliers start: 49 outliers final: 31 residues processed: 204 average time/residue: 0.3528 time to fit residues: 107.7455 Evaluate side-chains 198 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 19176 Z= 0.299 Angle : 0.500 4.543 25974 Z= 0.270 Chirality : 0.042 0.136 2904 Planarity : 0.004 0.035 3396 Dihedral : 3.937 15.069 2616 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.58 % Allowed : 12.61 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2448 helix: 2.54 (0.14), residues: 1224 sheet: 0.16 (0.31), residues: 354 loop : -1.80 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 348 HIS 0.005 0.001 HIS C 384 PHE 0.014 0.002 PHE A 374 TYR 0.010 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 2.131 Fit side-chains REVERT: A 303 LYS cc_start: 0.7104 (ptpt) cc_final: 0.6219 (pttt) REVERT: A 377 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8486 (mt) REVERT: B 87 MET cc_start: 0.9008 (tpp) cc_final: 0.8714 (tpp) REVERT: B 117 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 303 LYS cc_start: 0.7065 (ptpt) cc_final: 0.6436 (pttt) REVERT: B 377 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8453 (mt) REVERT: C 117 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 214 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: C 281 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6007 (mm-30) REVERT: C 303 LYS cc_start: 0.7019 (ptpt) cc_final: 0.6073 (pttt) REVERT: C 377 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8363 (mt) REVERT: C 381 CYS cc_start: 0.7817 (t) cc_final: 0.6998 (m) REVERT: D 253 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7778 (tt) REVERT: E 377 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8510 (mt) REVERT: F 272 MET cc_start: 0.6687 (tpt) cc_final: 0.6025 (mmt) REVERT: F 377 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8480 (mt) outliers start: 51 outliers final: 34 residues processed: 201 average time/residue: 0.3435 time to fit residues: 102.3332 Evaluate side-chains 204 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 238 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19176 Z= 0.256 Angle : 0.473 4.289 25974 Z= 0.256 Chirality : 0.041 0.135 2904 Planarity : 0.004 0.034 3396 Dihedral : 3.814 15.015 2616 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.84 % Allowed : 13.02 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2448 helix: 2.64 (0.14), residues: 1230 sheet: 0.05 (0.32), residues: 324 loop : -1.47 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.004 0.001 HIS B 384 PHE 0.013 0.002 PHE A 374 TYR 0.009 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 2.354 Fit side-chains REVERT: A 117 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 303 LYS cc_start: 0.7067 (ptpt) cc_final: 0.6265 (pttt) REVERT: A 377 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 87 MET cc_start: 0.9002 (tpp) cc_final: 0.8731 (tpp) REVERT: B 117 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 280 HIS cc_start: 0.7055 (m-70) cc_final: 0.6825 (m170) REVERT: B 303 LYS cc_start: 0.7064 (ptpt) cc_final: 0.6392 (pttt) REVERT: B 377 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8533 (mt) REVERT: C 117 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 214 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: C 303 LYS cc_start: 0.7043 (ptpt) cc_final: 0.6049 (pttt) REVERT: C 377 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (mt) REVERT: D 253 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (tt) REVERT: D 410 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: E 253 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7749 (tt) REVERT: E 377 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8506 (mt) REVERT: E 410 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: F 280 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7209 (t-90) REVERT: F 377 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8483 (mt) outliers start: 56 outliers final: 37 residues processed: 213 average time/residue: 0.3505 time to fit residues: 111.1972 Evaluate side-chains 212 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS D 212 GLN F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19176 Z= 0.158 Angle : 0.425 5.367 25974 Z= 0.230 Chirality : 0.039 0.132 2904 Planarity : 0.003 0.033 3396 Dihedral : 3.533 14.734 2616 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.28 % Allowed : 14.34 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2448 helix: 2.92 (0.14), residues: 1230 sheet: -0.03 (0.32), residues: 342 loop : -1.28 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.003 0.001 HIS D 161 PHE 0.016 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 2.015 Fit side-chains REVERT: A 303 LYS cc_start: 0.7093 (ptpt) cc_final: 0.6311 (pttt) REVERT: B 87 MET cc_start: 0.8894 (tpp) cc_final: 0.8460 (tpp) REVERT: B 303 LYS cc_start: 0.7028 (ptpt) cc_final: 0.6379 (pttt) REVERT: C 214 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: C 281 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6555 (mm-30) REVERT: C 303 LYS cc_start: 0.6977 (ptpt) cc_final: 0.6086 (pttt) REVERT: C 377 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8511 (mt) REVERT: D 253 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7811 (tt) REVERT: D 410 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6643 (mm-30) REVERT: E 253 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7709 (tt) REVERT: E 377 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8534 (mt) REVERT: F 280 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: F 377 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8478 (mt) outliers start: 45 outliers final: 28 residues processed: 202 average time/residue: 0.3812 time to fit residues: 114.2299 Evaluate side-chains 197 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 275 ASP Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19176 Z= 0.295 Angle : 0.494 6.075 25974 Z= 0.268 Chirality : 0.042 0.134 2904 Planarity : 0.004 0.034 3396 Dihedral : 3.790 14.874 2616 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.94 % Allowed : 13.88 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.17), residues: 2448 helix: 2.74 (0.14), residues: 1230 sheet: 0.19 (0.32), residues: 324 loop : -1.40 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.004 0.001 HIS B 384 PHE 0.017 0.002 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 2.474 Fit side-chains REVERT: A 281 GLU cc_start: 0.6383 (mm-30) cc_final: 0.6155 (mm-30) REVERT: A 303 LYS cc_start: 0.7158 (ptpt) cc_final: 0.6341 (pttt) REVERT: B 87 MET cc_start: 0.9005 (tpp) cc_final: 0.8722 (tpp) REVERT: B 280 HIS cc_start: 0.6857 (m-70) cc_final: 0.6270 (m-70) REVERT: B 303 LYS cc_start: 0.7075 (ptpt) cc_final: 0.6488 (pttt) REVERT: C 214 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: C 281 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6554 (mm-30) REVERT: C 303 LYS cc_start: 0.6947 (ptpt) cc_final: 0.6052 (pttt) REVERT: C 377 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8486 (mt) REVERT: D 253 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7773 (tt) REVERT: D 410 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: E 253 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7729 (tt) REVERT: E 377 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8459 (mt) REVERT: E 410 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: F 280 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.7187 (t-90) REVERT: F 377 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8464 (mt) outliers start: 58 outliers final: 39 residues processed: 208 average time/residue: 0.3548 time to fit residues: 109.4863 Evaluate side-chains 207 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 0.4980 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.189 Angle : 0.443 6.419 25974 Z= 0.239 Chirality : 0.040 0.133 2904 Planarity : 0.003 0.033 3396 Dihedral : 3.582 14.980 2616 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.63 % Allowed : 14.54 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2448 helix: 2.92 (0.14), residues: 1230 sheet: 0.13 (0.32), residues: 336 loop : -1.25 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.003 0.001 HIS B 384 PHE 0.019 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.007 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 2.112 Fit side-chains REVERT: A 303 LYS cc_start: 0.7129 (ptpt) cc_final: 0.6347 (pttt) REVERT: B 87 MET cc_start: 0.8937 (tpp) cc_final: 0.8709 (tpp) REVERT: B 280 HIS cc_start: 0.6815 (m-70) cc_final: 0.6269 (m-70) REVERT: B 303 LYS cc_start: 0.7094 (ptpt) cc_final: 0.6475 (pttt) REVERT: C 214 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: C 281 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6478 (mm-30) REVERT: C 303 LYS cc_start: 0.6921 (ptpt) cc_final: 0.6022 (pttt) REVERT: C 377 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 253 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7792 (tt) REVERT: D 410 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: E 253 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7660 (tt) REVERT: E 377 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8508 (mt) REVERT: E 410 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: F 280 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7142 (t-90) REVERT: F 377 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (mt) outliers start: 52 outliers final: 35 residues processed: 206 average time/residue: 0.3598 time to fit residues: 109.2152 Evaluate side-chains 204 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 HIS F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19176 Z= 0.277 Angle : 0.494 9.007 25974 Z= 0.265 Chirality : 0.042 0.135 2904 Planarity : 0.004 0.034 3396 Dihedral : 3.757 15.030 2616 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.48 % Allowed : 14.64 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2448 helix: 2.78 (0.14), residues: 1230 sheet: 0.26 (0.33), residues: 324 loop : -1.39 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.004 0.001 HIS B 384 PHE 0.024 0.002 PHE B 11 TYR 0.010 0.001 TYR A 51 ARG 0.006 0.000 ARG D 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 2.286 Fit side-chains REVERT: A 281 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6176 (mm-30) REVERT: A 303 LYS cc_start: 0.7183 (ptpt) cc_final: 0.6395 (pttt) REVERT: B 87 MET cc_start: 0.8992 (tpp) cc_final: 0.8713 (tpp) REVERT: B 280 HIS cc_start: 0.6906 (m-70) cc_final: 0.6330 (m-70) REVERT: B 281 GLU cc_start: 0.6465 (mm-30) cc_final: 0.6188 (mm-30) REVERT: B 303 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6483 (pttt) REVERT: C 214 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: C 303 LYS cc_start: 0.6957 (ptpt) cc_final: 0.6183 (pttt) REVERT: C 377 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 253 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7756 (tt) REVERT: D 410 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: E 253 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7691 (tt) REVERT: E 377 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8473 (mt) REVERT: E 410 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: F 280 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7234 (t-90) REVERT: F 377 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8458 (mt) outliers start: 49 outliers final: 38 residues processed: 200 average time/residue: 0.3687 time to fit residues: 109.9575 Evaluate side-chains 207 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 160 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN C 280 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.090578 restraints weight = 26107.093| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.55 r_work: 0.2859 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19176 Z= 0.166 Angle : 0.438 9.233 25974 Z= 0.235 Chirality : 0.039 0.133 2904 Planarity : 0.003 0.033 3396 Dihedral : 3.502 14.979 2616 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.33 % Allowed : 14.99 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2448 helix: 2.99 (0.14), residues: 1230 sheet: 0.21 (0.32), residues: 336 loop : -1.24 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.004 0.001 HIS D 256 PHE 0.023 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.07 seconds wall clock time: 67 minutes 55.10 seconds (4075.10 seconds total)