Starting phenix.real_space_refine on Mon Mar 18 14:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/03_2024/8bhw_16071.pdb" } resolution = 3.2 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= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13416 2.51 5 N 3800 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "D" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 12.31, per 1000 atoms: 0.58 Number of scatterers: 21240 At special positions: 0 Unit cell: (126.14, 126.14, 170.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3904 8.00 N 3800 7.00 C 13416 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: 8.85 Conformation dependent library (CDL) restraints added in 3.9 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 70.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.775A pdb=" N ARG A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.532A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.984A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 4.344A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.668A pdb=" N GLN A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.630A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 239 removed outlier: 3.616A pdb=" N ASN A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.587A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 348 removed outlier: 3.549A pdb=" N MET A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.748A pdb=" N ARG B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 removed outlier: 4.149A pdb=" N ALA B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.568A pdb=" N GLY B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 121 removed outlier: 3.522A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.638A pdb=" N LYS B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.586A pdb=" N ASN B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 238 removed outlier: 3.972A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.551A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 348 Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.779A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 50 removed outlier: 3.555A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.897A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 4.273A pdb=" N SER C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.662A pdb=" N GLN C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.630A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 239 removed outlier: 3.554A pdb=" N ASN C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.586A pdb=" N ASP C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.535A pdb=" N ARG C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.973A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 50 removed outlier: 4.121A pdb=" N ALA D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 47 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.570A pdb=" N GLY D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.555A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.809A pdb=" N LYS D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.585A pdb=" N ASN D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 removed outlier: 3.971A pdb=" N LEU D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.577A pdb=" N ASP D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 348 Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.806A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.567A pdb=" N ILE E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.861A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 86 removed outlier: 4.256A pdb=" N SER E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 removed outlier: 3.513A pdb=" N SER E 110 " --> pdb=" O MET E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 removed outlier: 3.629A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 167 through 239 removed outlier: 3.550A pdb=" N ASN E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.603A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 347 removed outlier: 3.670A pdb=" N ARG E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.838A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 50 removed outlier: 3.513A pdb=" N LEU F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR F 47 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.563A pdb=" N GLY F 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 83 Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.521A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.719A pdb=" N LYS F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.581A pdb=" N ASN F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 removed outlier: 3.970A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.557A pdb=" N ASP F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 348 Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.698A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.837A pdb=" N LEU G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.870A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 removed outlier: 4.267A pdb=" N SER G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.652A pdb=" N GLN G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.623A pdb=" N ILE G 146 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 239 removed outlier: 3.615A pdb=" N ASN G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 260 through 275 Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.585A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 347 removed outlier: 3.649A pdb=" N ILE G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.835A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 50 removed outlier: 4.167A pdb=" N ALA H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR H 47 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 70 removed outlier: 3.571A pdb=" N GLY H 70 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 83 Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 121 removed outlier: 3.553A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.801A pdb=" N LYS H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.589A pdb=" N ASN H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 238 removed outlier: 3.972A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.558A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 348 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.256A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 147 through 149 removed outlier: 6.806A pdb=" N ASP B 62 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR B 307 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 147 through 149 removed outlier: 6.258A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 147 through 149 removed outlier: 6.791A pdb=" N ASP D 62 " --> pdb=" O TYR D 307 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR D 307 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.246A pdb=" N ILE E 60 " --> pdb=" O LEU E 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 147 through 149 removed outlier: 6.790A pdb=" N ASP F 62 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR F 307 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 147 through 149 removed outlier: 6.258A pdb=" N ILE G 60 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 147 through 149 removed outlier: 6.780A pdb=" N ASP H 62 " --> pdb=" O TYR H 307 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR H 307 " --> pdb=" O ASP H 62 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 4242 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: 6.06 Time building geometry restraints manager: 9.50 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: 7188 1.34 - 1.46: 4811 1.46 - 1.58: 9433 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21664 Sorted by residual: bond pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB ARG H 85 " pdb=" CG ARG H 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" CB ARG D 85 " pdb=" CG ARG D 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" CB ARG F 85 " pdb=" CG ARG F 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.54e-01 ... (remaining 21659 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 461 105.89 - 112.93: 11374 112.93 - 119.96: 7462 119.96 - 127.00: 9772 127.00 - 134.03: 243 Bond angle restraints: 29312 Sorted by residual: angle pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " ideal model delta sigma weight residual 112.70 123.06 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CB MET B 224 " pdb=" CG MET B 224 " pdb=" SD MET B 224 " ideal model delta sigma weight residual 112.70 122.74 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET H 263 " pdb=" CG MET H 263 " pdb=" SD MET H 263 " ideal model delta sigma weight residual 112.70 122.26 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET D 263 " pdb=" CG MET D 263 " pdb=" SD MET D 263 " ideal model delta sigma weight residual 112.70 122.26 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB ARG E 85 " pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 111.30 118.45 -7.15 2.30e+00 1.89e-01 9.67e+00 ... (remaining 29307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 11270 17.00 - 34.00: 1420 34.00 - 51.00: 389 51.00 - 68.00: 70 68.00 - 85.00: 19 Dihedral angle restraints: 13168 sinusoidal: 5392 harmonic: 7776 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" CB ASP A 62 " pdb=" CG ASP A 62 " pdb=" OD1 ASP A 62 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP E 62 " pdb=" CB ASP E 62 " pdb=" CG ASP E 62 " pdb=" OD1 ASP E 62 " ideal model delta sinusoidal sigma weight residual -30.00 -87.92 57.92 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 62 " pdb=" CB ASP C 62 " pdb=" CG ASP C 62 " pdb=" OD1 ASP C 62 " ideal model delta sinusoidal sigma weight residual -30.00 -87.90 57.90 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 13165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1918 0.025 - 0.050: 833 0.050 - 0.075: 287 0.075 - 0.100: 96 0.100 - 0.125: 50 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CA ARG G 301 " pdb=" N ARG G 301 " pdb=" C ARG G 301 " pdb=" CB ARG G 301 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 149 " pdb=" N ILE B 149 " pdb=" C ILE B 149 " pdb=" CB ILE B 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ARG C 301 " pdb=" N ARG C 301 " pdb=" C ARG C 301 " pdb=" CB ARG C 301 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 3181 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 319 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO E 320 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 320 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 320 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 319 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO C 320 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 247 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.015 5.00e-02 4.00e+02 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1139 2.73 - 3.27: 21538 3.27 - 3.82: 36251 3.82 - 4.36: 38042 4.36 - 4.90: 68509 Nonbonded interactions: 165479 Sorted by model distance: nonbonded pdb=" O LEU E 108 " pdb=" OH TYR E 178 " model vdw 2.188 2.440 nonbonded pdb=" O LEU G 108 " pdb=" OH TYR G 178 " model vdw 2.190 2.440 nonbonded pdb=" O LEU A 108 " pdb=" OH TYR A 178 " model vdw 2.191 2.440 nonbonded pdb=" O LEU C 108 " pdb=" OH TYR C 178 " model vdw 2.192 2.440 nonbonded pdb=" OD1 ASP C 83 " pdb=" NH2 ARG C 201 " model vdw 2.235 2.520 ... (remaining 165474 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' selection = chain 'G' selection = chain 'H' } 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.430 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 57.630 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.110 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.003 0.031 21664 Z= 0.194 Angle : 0.561 10.356 29312 Z= 0.280 Chirality : 0.034 0.125 3184 Planarity : 0.003 0.035 3840 Dihedral : 16.119 85.004 8128 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.18 % Allowed : 19.16 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2640 helix: 3.26 (0.13), residues: 1648 sheet: 2.23 (0.48), residues: 156 loop : -0.71 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.002 0.000 HIS E 237 PHE 0.015 0.001 PHE G 153 TYR 0.013 0.001 TYR E 123 ARG 0.006 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 75 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8415 (mm-40) REVERT: F 75 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: G 68 MET cc_start: 0.9153 (ttm) cc_final: 0.8857 (ttm) REVERT: G 97 MET cc_start: 0.9056 (mpp) cc_final: 0.8745 (mmm) outliers start: 4 outliers final: 2 residues processed: 132 average time/residue: 0.3446 time to fit residues: 70.6511 Evaluate side-chains 130 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21664 Z= 0.333 Angle : 0.561 7.169 29312 Z= 0.291 Chirality : 0.037 0.154 3184 Planarity : 0.003 0.040 3840 Dihedral : 4.091 61.431 2971 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.13 % Allowed : 19.29 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.17), residues: 2640 helix: 3.28 (0.12), residues: 1760 sheet: 1.81 (0.47), residues: 156 loop : -0.71 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.002 0.001 HIS C 237 PHE 0.014 0.001 PHE H 181 TYR 0.012 0.002 TYR A 123 ARG 0.004 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8344 (mtt180) REVERT: A 272 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.9188 (mt0) REVERT: D 224 MET cc_start: 0.8953 (tpp) cc_final: 0.8627 (tpp) REVERT: E 68 MET cc_start: 0.9117 (ttm) cc_final: 0.8783 (ttm) REVERT: E 272 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9218 (mt0) REVERT: E 301 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.9055 (ttp80) REVERT: F 75 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8763 (mm-40) REVERT: F 224 MET cc_start: 0.8995 (tpp) cc_final: 0.8654 (tpp) REVERT: G 36 MET cc_start: 0.5377 (ppp) cc_final: 0.5066 (ppp) REVERT: G 68 MET cc_start: 0.9094 (ttm) cc_final: 0.8762 (ttm) REVERT: G 155 ARG cc_start: 0.9335 (mtp-110) cc_final: 0.9080 (mtm110) REVERT: G 272 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9195 (mt0) REVERT: H 224 MET cc_start: 0.8931 (tpp) cc_final: 0.8612 (tpp) outliers start: 47 outliers final: 25 residues processed: 173 average time/residue: 0.3452 time to fit residues: 91.7556 Evaluate side-chains 158 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 237 HIS Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 30.0000 chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 240 optimal weight: 0.6980 chunk 259 optimal weight: 0.0980 chunk 213 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21664 Z= 0.145 Angle : 0.471 7.162 29312 Z= 0.244 Chirality : 0.034 0.143 3184 Planarity : 0.003 0.039 3840 Dihedral : 3.602 61.471 2963 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.77 % Allowed : 19.57 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.17), residues: 2640 helix: 3.29 (0.12), residues: 1784 sheet: 2.01 (0.48), residues: 156 loop : -0.72 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 32 HIS 0.002 0.000 HIS E 237 PHE 0.009 0.001 PHE A 40 TYR 0.012 0.001 TYR A 123 ARG 0.008 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8984 (mpp) cc_final: 0.8687 (mmm) REVERT: B 224 MET cc_start: 0.8912 (tpp) cc_final: 0.8557 (tpp) REVERT: C 68 MET cc_start: 0.9151 (ttm) cc_final: 0.8863 (ttp) REVERT: C 97 MET cc_start: 0.9004 (mpp) cc_final: 0.8632 (mmm) REVERT: D 75 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8692 (mm-40) REVERT: D 224 MET cc_start: 0.8938 (tpp) cc_final: 0.8540 (tpp) REVERT: E 68 MET cc_start: 0.9169 (ttm) cc_final: 0.8880 (ttp) REVERT: F 224 MET cc_start: 0.8956 (tpp) cc_final: 0.8561 (tpp) REVERT: G 36 MET cc_start: 0.4916 (ppp) cc_final: 0.4648 (ppp) REVERT: G 68 MET cc_start: 0.9142 (ttm) cc_final: 0.8868 (ttp) REVERT: G 97 MET cc_start: 0.8972 (mpp) cc_final: 0.8682 (mmm) REVERT: G 224 MET cc_start: 0.8976 (tpp) cc_final: 0.8764 (tpp) REVERT: H 224 MET cc_start: 0.8922 (tpp) cc_final: 0.8539 (tpp) outliers start: 39 outliers final: 24 residues processed: 169 average time/residue: 0.3345 time to fit residues: 86.9345 Evaluate side-chains 151 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21664 Z= 0.167 Angle : 0.482 7.197 29312 Z= 0.245 Chirality : 0.034 0.144 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.339 13.644 2960 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.72 % Allowed : 20.29 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.17), residues: 2640 helix: 3.36 (0.12), residues: 1784 sheet: 2.41 (0.58), residues: 112 loop : -0.73 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 111 HIS 0.001 0.000 HIS B 189 PHE 0.016 0.001 PHE C 40 TYR 0.011 0.001 TYR A 123 ARG 0.006 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (mtt180) REVERT: B 224 MET cc_start: 0.8930 (tpp) cc_final: 0.8508 (tpp) REVERT: C 68 MET cc_start: 0.9154 (ttm) cc_final: 0.8862 (ttp) REVERT: D 224 MET cc_start: 0.8902 (tpp) cc_final: 0.8480 (tpp) REVERT: E 36 MET cc_start: 0.7127 (ppp) cc_final: 0.6444 (ppp) REVERT: E 68 MET cc_start: 0.9178 (ttm) cc_final: 0.8887 (ttp) REVERT: F 224 MET cc_start: 0.8935 (tpp) cc_final: 0.8496 (tpp) REVERT: G 36 MET cc_start: 0.4685 (ppp) cc_final: 0.4394 (ppp) REVERT: G 68 MET cc_start: 0.9157 (ttm) cc_final: 0.8876 (ttp) REVERT: H 224 MET cc_start: 0.8936 (tpp) cc_final: 0.8525 (tpp) outliers start: 38 outliers final: 29 residues processed: 164 average time/residue: 0.3475 time to fit residues: 87.7195 Evaluate side-chains 156 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 64 optimal weight: 40.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21664 Z= 0.258 Angle : 0.508 8.877 29312 Z= 0.258 Chirality : 0.035 0.143 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.350 13.369 2960 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.22 % Allowed : 19.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2640 helix: 3.42 (0.12), residues: 1784 sheet: 2.27 (0.58), residues: 112 loop : -0.70 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 111 HIS 0.001 0.001 HIS B 189 PHE 0.011 0.001 PHE H 181 TYR 0.012 0.001 TYR G 123 ARG 0.007 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8271 (mtt180) REVERT: A 97 MET cc_start: 0.9031 (mpp) cc_final: 0.8744 (mmm) REVERT: A 272 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.9252 (mt0) REVERT: B 224 MET cc_start: 0.8920 (tpp) cc_final: 0.8478 (tpp) REVERT: C 68 MET cc_start: 0.9149 (ttm) cc_final: 0.8861 (ttp) REVERT: C 97 MET cc_start: 0.9021 (mpp) cc_final: 0.8688 (mmm) REVERT: D 75 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: D 224 MET cc_start: 0.8911 (tpp) cc_final: 0.8431 (tpp) REVERT: E 36 MET cc_start: 0.7019 (ppp) cc_final: 0.6582 (ppp) REVERT: E 68 MET cc_start: 0.9124 (ttm) cc_final: 0.8781 (ttm) REVERT: E 272 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9200 (mt0) REVERT: F 224 MET cc_start: 0.8938 (tpp) cc_final: 0.8447 (tpp) REVERT: G 36 MET cc_start: 0.4610 (ppp) cc_final: 0.4279 (ppp) REVERT: G 68 MET cc_start: 0.9148 (ttm) cc_final: 0.8861 (ttp) REVERT: G 97 MET cc_start: 0.9023 (mpp) cc_final: 0.8755 (mmm) REVERT: H 224 MET cc_start: 0.8892 (tpp) cc_final: 0.8457 (tpp) outliers start: 49 outliers final: 38 residues processed: 177 average time/residue: 0.3323 time to fit residues: 90.7151 Evaluate side-chains 168 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 134 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21664 Z= 0.143 Angle : 0.471 8.473 29312 Z= 0.238 Chirality : 0.034 0.143 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.304 14.262 2960 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.77 % Allowed : 20.88 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.17), residues: 2640 helix: 3.49 (0.12), residues: 1784 sheet: 2.49 (0.59), residues: 112 loop : -0.71 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 111 HIS 0.001 0.000 HIS F 189 PHE 0.009 0.001 PHE G 153 TYR 0.012 0.001 TYR A 123 ARG 0.008 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8392 (mtt180) REVERT: A 97 MET cc_start: 0.9001 (mpp) cc_final: 0.8698 (mmm) REVERT: A 155 ARG cc_start: 0.9390 (mtp-110) cc_final: 0.8939 (mtm110) REVERT: B 224 MET cc_start: 0.8943 (tpp) cc_final: 0.8473 (tpp) REVERT: C 68 MET cc_start: 0.9189 (ttm) cc_final: 0.8891 (ttp) REVERT: C 97 MET cc_start: 0.8972 (mpp) cc_final: 0.8628 (mmm) REVERT: D 224 MET cc_start: 0.8892 (tpp) cc_final: 0.8410 (tpp) REVERT: E 36 MET cc_start: 0.6966 (ppp) cc_final: 0.6506 (ppp) REVERT: E 68 MET cc_start: 0.9174 (ttm) cc_final: 0.8881 (ttp) REVERT: F 224 MET cc_start: 0.8931 (tpp) cc_final: 0.8430 (tpp) REVERT: G 36 MET cc_start: 0.4494 (ppp) cc_final: 0.4146 (ppp) REVERT: G 68 MET cc_start: 0.9173 (ttm) cc_final: 0.8867 (ttp) REVERT: G 97 MET cc_start: 0.8970 (mpp) cc_final: 0.8691 (mmm) REVERT: G 272 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9186 (mt0) REVERT: H 224 MET cc_start: 0.8949 (tpp) cc_final: 0.8485 (tpp) outliers start: 39 outliers final: 34 residues processed: 165 average time/residue: 0.3333 time to fit residues: 85.2174 Evaluate side-chains 162 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21664 Z= 0.154 Angle : 0.477 8.758 29312 Z= 0.239 Chirality : 0.034 0.141 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.269 14.083 2960 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.90 % Allowed : 21.11 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.17), residues: 2640 helix: 3.54 (0.12), residues: 1784 sheet: 2.42 (0.59), residues: 112 loop : -0.73 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 111 HIS 0.001 0.000 HIS F 189 PHE 0.008 0.001 PHE H 181 TYR 0.011 0.001 TYR A 123 ARG 0.007 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (mtt180) REVERT: B 224 MET cc_start: 0.8955 (tpp) cc_final: 0.8463 (tpp) REVERT: C 68 MET cc_start: 0.9194 (ttm) cc_final: 0.8897 (ttp) REVERT: D 88 MET cc_start: 0.7992 (mmp) cc_final: 0.7643 (mmp) REVERT: D 224 MET cc_start: 0.8871 (tpp) cc_final: 0.8363 (tpp) REVERT: E 36 MET cc_start: 0.6978 (ppp) cc_final: 0.6577 (ppp) REVERT: E 68 MET cc_start: 0.9179 (ttm) cc_final: 0.8890 (ttp) REVERT: E 142 MET cc_start: 0.8936 (mtm) cc_final: 0.8706 (mtm) REVERT: F 88 MET cc_start: 0.8006 (mmp) cc_final: 0.7666 (mmp) REVERT: F 224 MET cc_start: 0.8939 (tpp) cc_final: 0.8425 (tpp) REVERT: G 36 MET cc_start: 0.4457 (ppp) cc_final: 0.4103 (ppp) REVERT: G 68 MET cc_start: 0.9180 (ttm) cc_final: 0.8896 (ttm) REVERT: G 97 MET cc_start: 0.8965 (mpp) cc_final: 0.8688 (mmm) REVERT: G 272 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9196 (mt0) REVERT: H 88 MET cc_start: 0.7961 (mmp) cc_final: 0.7590 (mmp) REVERT: H 224 MET cc_start: 0.8925 (tpp) cc_final: 0.8471 (tpp) outliers start: 42 outliers final: 38 residues processed: 167 average time/residue: 0.3222 time to fit residues: 84.9506 Evaluate side-chains 166 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21664 Z= 0.175 Angle : 0.485 7.984 29312 Z= 0.242 Chirality : 0.034 0.141 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.254 13.570 2960 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.04 % Allowed : 20.74 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.17), residues: 2640 helix: 3.60 (0.12), residues: 1788 sheet: 1.95 (0.48), residues: 156 loop : -0.67 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 111 HIS 0.001 0.000 HIS F 189 PHE 0.009 0.001 PHE H 181 TYR 0.011 0.001 TYR A 123 ARG 0.008 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8297 (mtt180) REVERT: A 97 MET cc_start: 0.9070 (mpp) cc_final: 0.8852 (mmm) REVERT: B 88 MET cc_start: 0.8102 (mmp) cc_final: 0.7804 (mmp) REVERT: B 224 MET cc_start: 0.8931 (tpp) cc_final: 0.8433 (tpp) REVERT: C 36 MET cc_start: 0.7212 (ppp) cc_final: 0.6527 (ppp) REVERT: C 68 MET cc_start: 0.9160 (ttm) cc_final: 0.8849 (ttp) REVERT: C 97 MET cc_start: 0.9033 (mpp) cc_final: 0.8790 (mmm) REVERT: D 88 MET cc_start: 0.7981 (mmp) cc_final: 0.7778 (mmp) REVERT: D 224 MET cc_start: 0.8897 (tpp) cc_final: 0.8385 (tpp) REVERT: E 36 MET cc_start: 0.6735 (ppp) cc_final: 0.6400 (ppp) REVERT: E 68 MET cc_start: 0.9166 (ttm) cc_final: 0.8865 (ttp) REVERT: E 272 GLN cc_start: 0.9489 (OUTLIER) cc_final: 0.9176 (mt0) REVERT: F 88 MET cc_start: 0.7998 (mmp) cc_final: 0.7776 (mmp) REVERT: F 224 MET cc_start: 0.8945 (tpp) cc_final: 0.8439 (tpp) REVERT: G 36 MET cc_start: 0.4615 (ppp) cc_final: 0.4207 (ppp) REVERT: G 68 MET cc_start: 0.9180 (ttm) cc_final: 0.8893 (ttp) REVERT: G 224 MET cc_start: 0.8989 (tpp) cc_final: 0.8750 (tpp) REVERT: H 88 MET cc_start: 0.7958 (mmp) cc_final: 0.7753 (mmp) REVERT: H 224 MET cc_start: 0.8923 (tpp) cc_final: 0.8451 (tpp) outliers start: 45 outliers final: 42 residues processed: 171 average time/residue: 0.3436 time to fit residues: 90.7729 Evaluate side-chains 169 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9990 chunk 222 optimal weight: 0.3980 chunk 237 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21664 Z= 0.156 Angle : 0.479 7.869 29312 Z= 0.238 Chirality : 0.034 0.142 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.230 13.350 2960 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 20.74 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.17), residues: 2640 helix: 3.63 (0.12), residues: 1788 sheet: 2.41 (0.59), residues: 112 loop : -0.72 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 111 HIS 0.001 0.000 HIS F 189 PHE 0.010 0.001 PHE C 153 TYR 0.011 0.001 TYR A 123 ARG 0.005 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8391 (mtt180) REVERT: A 97 MET cc_start: 0.9021 (mpp) cc_final: 0.8747 (mmm) REVERT: A 224 MET cc_start: 0.8960 (tpp) cc_final: 0.8742 (tpp) REVERT: B 88 MET cc_start: 0.8075 (mmp) cc_final: 0.7813 (mmp) REVERT: B 224 MET cc_start: 0.8930 (tpp) cc_final: 0.8420 (tpp) REVERT: C 36 MET cc_start: 0.7054 (ppp) cc_final: 0.6396 (ppp) REVERT: C 68 MET cc_start: 0.9183 (ttm) cc_final: 0.8884 (ttp) REVERT: C 97 MET cc_start: 0.8983 (mpp) cc_final: 0.8690 (mmm) REVERT: D 224 MET cc_start: 0.8896 (tpp) cc_final: 0.8367 (tpp) REVERT: E 36 MET cc_start: 0.6681 (ppp) cc_final: 0.6354 (ppp) REVERT: E 68 MET cc_start: 0.9182 (ttm) cc_final: 0.8876 (ttp) REVERT: E 106 MET cc_start: 0.9191 (ttp) cc_final: 0.8980 (ttp) REVERT: F 224 MET cc_start: 0.8962 (tpp) cc_final: 0.8464 (tpp) REVERT: G 36 MET cc_start: 0.4498 (ppp) cc_final: 0.4079 (ppp) REVERT: G 68 MET cc_start: 0.9175 (ttm) cc_final: 0.8880 (ttp) REVERT: H 224 MET cc_start: 0.8922 (tpp) cc_final: 0.8441 (tpp) outliers start: 45 outliers final: 42 residues processed: 168 average time/residue: 0.3232 time to fit residues: 85.7696 Evaluate side-chains 169 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 40.0000 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.0980 chunk 128 optimal weight: 0.0020 chunk 166 optimal weight: 8.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 GLN C 144 ASN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21664 Z= 0.146 Angle : 0.483 10.355 29312 Z= 0.239 Chirality : 0.034 0.138 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.197 12.770 2960 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.95 % Allowed : 21.01 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.17), residues: 2640 helix: 3.66 (0.12), residues: 1788 sheet: 2.46 (0.60), residues: 112 loop : -0.72 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 111 HIS 0.001 0.000 HIS F 189 PHE 0.010 0.001 PHE G 153 TYR 0.011 0.001 TYR A 123 ARG 0.005 0.000 ARG C 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8340 (mtt180) REVERT: A 85 ARG cc_start: 0.9318 (mmp80) cc_final: 0.9101 (mmp80) REVERT: A 97 MET cc_start: 0.9033 (mpp) cc_final: 0.8790 (mmm) REVERT: B 88 MET cc_start: 0.8078 (mmp) cc_final: 0.7860 (mmp) REVERT: B 224 MET cc_start: 0.8940 (tpp) cc_final: 0.8426 (tpp) REVERT: C 36 MET cc_start: 0.7081 (ppp) cc_final: 0.6526 (ppp) REVERT: C 68 MET cc_start: 0.9204 (ttm) cc_final: 0.8897 (ttp) REVERT: C 97 MET cc_start: 0.8966 (mpp) cc_final: 0.8692 (mmm) REVERT: D 68 MET cc_start: 0.9129 (pmm) cc_final: 0.8646 (pmm) REVERT: D 224 MET cc_start: 0.8924 (tpp) cc_final: 0.8387 (tpp) REVERT: E 36 MET cc_start: 0.6448 (ppp) cc_final: 0.6085 (ppp) REVERT: E 68 MET cc_start: 0.9179 (ttm) cc_final: 0.8877 (ttp) REVERT: E 106 MET cc_start: 0.9188 (ttp) cc_final: 0.8978 (ttp) REVERT: E 272 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9191 (mt0) REVERT: F 68 MET cc_start: 0.9131 (pmm) cc_final: 0.8648 (pmm) REVERT: F 224 MET cc_start: 0.8962 (tpp) cc_final: 0.8472 (tpp) REVERT: G 36 MET cc_start: 0.4174 (ppp) cc_final: 0.3735 (ppp) REVERT: G 68 MET cc_start: 0.9188 (ttm) cc_final: 0.8882 (ttp) REVERT: H 224 MET cc_start: 0.8928 (tpp) cc_final: 0.8444 (tpp) outliers start: 43 outliers final: 40 residues processed: 168 average time/residue: 0.3483 time to fit residues: 90.6783 Evaluate side-chains 168 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 215 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053198 restraints weight = 81077.137| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.45 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21664 Z= 0.244 Angle : 0.520 9.375 29312 Z= 0.259 Chirality : 0.035 0.138 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.272 13.931 2960 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.04 % Allowed : 21.20 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.17), residues: 2640 helix: 3.76 (0.12), residues: 1736 sheet: 2.26 (0.59), residues: 112 loop : -0.72 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.001 0.001 HIS F 189 PHE 0.012 0.001 PHE D 181 TYR 0.011 0.001 TYR A 123 ARG 0.009 0.000 ARG D 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3345.78 seconds wall clock time: 64 minutes 17.35 seconds (3857.35 seconds total)