Starting phenix.real_space_refine on Sat Feb 17 01:04:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wht_32511/02_2024/7wht_32511_updated.pdb" } resolution = 3.5 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= 0.051 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 10806 2.51 5 N 2910 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F GLU 374": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16980 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "C" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "D" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "E" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "F" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.68, per 1000 atoms: 0.51 Number of scatterers: 16980 At special positions: 0 Unit cell: (120.91, 121.98, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 Mg 6 11.99 O 3144 8.00 N 2910 7.00 C 10806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 2.9 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 31 sheets defined 16.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 41 through 51 removed outlier: 4.502A pdb=" N GLN A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.763A pdb=" N MET A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.985A pdb=" N LEU A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 removed outlier: 3.521A pdb=" N GLN A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 230 through 244 Proline residue: A 242 - end of helix Processing helix chain 'B' and resid 23 through 26 No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.877A pdb=" N GLN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.760A pdb=" N MET B 68 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.970A pdb=" N LEU B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.985A pdb=" N GLN B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 191 No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 230 through 244 Proline residue: B 242 - end of helix Processing helix chain 'C' and resid 23 through 26 No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.934A pdb=" N GLN C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 removed outlier: 3.802A pdb=" N MET C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.965A pdb=" N LEU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 107 removed outlier: 3.799A pdb=" N GLN C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 191 No H-bonds generated for 'chain 'C' and resid 188 through 191' Processing helix chain 'C' and resid 230 through 244 Proline residue: C 242 - end of helix Processing helix chain 'D' and resid 23 through 26 No H-bonds generated for 'chain 'D' and resid 23 through 26' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.943A pdb=" N GLN D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.728A pdb=" N MET D 68 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS D 69 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER D 76 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 4.007A pdb=" N LEU D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.698A pdb=" N GLN D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 230 through 244 Proline residue: D 242 - end of helix Processing helix chain 'E' and resid 23 through 26 No H-bonds generated for 'chain 'E' and resid 23 through 26' Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.840A pdb=" N GLN E 45 " --> pdb=" O MET E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 removed outlier: 3.700A pdb=" N MET E 68 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 69 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 3.967A pdb=" N LEU E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 removed outlier: 3.743A pdb=" N GLN E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 137 No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 188 through 191 No H-bonds generated for 'chain 'E' and resid 188 through 191' Processing helix chain 'E' and resid 230 through 244 Proline residue: E 242 - end of helix Processing helix chain 'F' and resid 23 through 26 No H-bonds generated for 'chain 'F' and resid 23 through 26' Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.897A pdb=" N GLN F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 73 removed outlier: 3.692A pdb=" N MET F 68 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS F 69 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 3.960A pdb=" N LEU F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.775A pdb=" N GLN F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'F' and resid 230 through 244 Proline residue: F 242 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 removed outlier: 7.249A pdb=" N GLU A 56 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE A 13 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 58 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER A 82 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 119 through 121 Processing sheet with id= C, first strand: chain 'A' and resid 304 through 306 Processing sheet with id= D, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= E, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.606A pdb=" N GLY A 376 " --> pdb=" O LYS A 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 183 through 186 removed outlier: 6.983A pdb=" N ARG B 10 " --> pdb=" O PHE B 113 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU B 115 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 12 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU B 56 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 13 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 58 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER B 82 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 119 through 121 Processing sheet with id= H, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.170A pdb=" N ALA B 291 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 304 through 306 Processing sheet with id= J, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= K, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.757A pdb=" N GLY B 376 " --> pdb=" O LYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 183 through 186 removed outlier: 7.035A pdb=" N ARG C 10 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU C 115 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL C 12 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 56 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE C 13 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 58 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER C 82 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 119 through 121 Processing sheet with id= N, first strand: chain 'C' and resid 304 through 306 Processing sheet with id= O, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= P, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.752A pdb=" N GLY C 376 " --> pdb=" O LYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 183 through 186 removed outlier: 7.268A pdb=" N GLU D 56 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE D 13 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 58 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER D 82 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 119 through 121 Processing sheet with id= S, first strand: chain 'D' and resid 304 through 306 Processing sheet with id= T, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= U, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.699A pdb=" N GLY D 376 " --> pdb=" O LYS D 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 183 through 186 removed outlier: 7.047A pdb=" N ARG E 10 " --> pdb=" O PHE E 113 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU E 115 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL E 12 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU E 56 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE E 13 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE E 58 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER E 82 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 119 through 121 Processing sheet with id= X, first strand: chain 'E' and resid 273 through 275 removed outlier: 6.217A pdb=" N ALA E 291 " --> pdb=" O LEU E 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 304 through 306 Processing sheet with id= Z, first strand: chain 'E' and resid 338 through 340 Processing sheet with id= AA, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.762A pdb=" N GLY E 376 " --> pdb=" O LYS E 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 183 through 186 removed outlier: 7.046A pdb=" N ARG F 10 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU F 115 " --> pdb=" O ARG F 10 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 12 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU F 56 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE F 13 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 58 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER F 82 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 119 through 121 Processing sheet with id= AD, first strand: chain 'F' and resid 338 through 340 Processing sheet with id= AE, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.781A pdb=" N GLY F 376 " --> pdb=" O LYS F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE 196 hydrogen bonds defined for protein. 486 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: 4.46 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3607 1.33 - 1.45: 3690 1.45 - 1.57: 9845 1.57 - 1.69: 24 1.69 - 1.81: 174 Bond restraints: 17340 Sorted by residual: bond pdb=" CA TRP A 224 " pdb=" C TRP A 224 " ideal model delta sigma weight residual 1.521 1.450 0.070 1.26e-02 6.30e+03 3.13e+01 bond pdb=" CA TRP D 224 " pdb=" C TRP D 224 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.28e-02 6.10e+03 2.69e+01 bond pdb=" CA PHE E 223 " pdb=" C PHE E 223 " ideal model delta sigma weight residual 1.526 1.461 0.065 1.37e-02 5.33e+03 2.26e+01 bond pdb=" CA PHE B 223 " pdb=" C PHE B 223 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.15e+01 bond pdb=" CA PHE F 223 " pdb=" C PHE F 223 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.13e+01 ... (remaining 17335 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.94: 570 105.94 - 113.76: 9817 113.76 - 121.58: 8821 121.58 - 129.40: 4160 129.40 - 137.22: 128 Bond angle restraints: 23496 Sorted by residual: angle pdb=" N ALA A 210 " pdb=" CA ALA A 210 " pdb=" C ALA A 210 " ideal model delta sigma weight residual 111.36 122.44 -11.08 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N ALA A 211 " pdb=" CA ALA A 211 " pdb=" C ALA A 211 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.58e+00 4.01e-01 7.04e+01 angle pdb=" N HIS A 132 " pdb=" CA HIS A 132 " pdb=" C HIS A 132 " ideal model delta sigma weight residual 111.36 103.61 7.75 1.09e+00 8.42e-01 5.06e+01 angle pdb=" N GLU D 212 " pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 108.60 118.70 -10.10 1.46e+00 4.69e-01 4.78e+01 angle pdb=" N ALA C 208 " pdb=" CA ALA C 208 " pdb=" C ALA C 208 " ideal model delta sigma weight residual 111.28 118.74 -7.46 1.09e+00 8.42e-01 4.68e+01 ... (remaining 23491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.90: 9838 25.90 - 51.80: 612 51.80 - 77.70: 73 77.70 - 103.60: 25 103.60 - 129.50: 42 Dihedral angle restraints: 10590 sinusoidal: 4512 harmonic: 6078 Sorted by residual: dihedral pdb=" C GLU E 212 " pdb=" N GLU E 212 " pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " ideal model delta harmonic sigma weight residual -122.60 -133.79 11.19 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" N GLU E 212 " pdb=" C GLU E 212 " pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " ideal model delta harmonic sigma weight residual 122.80 133.75 -10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" N ALA B 211 " pdb=" C ALA B 211 " pdb=" CA ALA B 211 " pdb=" CB ALA B 211 " ideal model delta harmonic sigma weight residual 122.90 133.76 -10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 10587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2242 0.090 - 0.180: 361 0.180 - 0.271: 23 0.271 - 0.361: 10 0.361 - 0.451: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CA ALA B 211 " pdb=" N ALA B 211 " pdb=" C ALA B 211 " pdb=" CB ALA B 211 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA GLU E 212 " pdb=" N GLU E 212 " pdb=" C GLU E 212 " pdb=" CB GLU E 212 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA ALA A 134 " pdb=" N ALA A 134 " pdb=" C ALA A 134 " pdb=" CB ALA A 134 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 2637 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 140 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C THR D 140 " -0.080 2.00e-02 2.50e+03 pdb=" O THR D 140 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE D 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 206 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO F 207 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 206 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO E 207 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 207 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 207 " 0.059 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 19 2.16 - 2.84: 5675 2.84 - 3.53: 23323 3.53 - 4.21: 39247 4.21 - 4.90: 68528 Nonbonded interactions: 136792 Sorted by model distance: nonbonded pdb=" O PHE C 131 " pdb=" OE1 GLU C 212 " model vdw 1.473 3.040 nonbonded pdb=" NH2 ARG D 193 " pdb=" NE2 GLN D 214 " model vdw 1.629 3.200 nonbonded pdb=" SD MET A 209 " pdb=" NE2 GLN A 214 " model vdw 1.635 2.880 nonbonded pdb=" CE MET A 209 " pdb=" NE2 GLN A 214 " model vdw 1.864 3.540 nonbonded pdb=" NH2 ARG D 193 " pdb=" OE1 GLN D 214 " model vdw 1.956 2.520 ... (remaining 136787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.480 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 44.260 Find NCS groups from input model: 1.150 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17340 Z= 0.380 Angle : 0.902 13.259 23496 Z= 0.455 Chirality : 0.061 0.451 2640 Planarity : 0.007 0.104 2988 Dihedral : 18.722 129.497 6690 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.38 % Allowed : 0.88 % Favored : 97.74 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2112 helix: 0.73 (0.35), residues: 264 sheet: 0.12 (0.28), residues: 348 loop : -1.53 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 329 HIS 0.005 0.001 HIS A 135 PHE 0.018 0.001 PHE E 223 TYR 0.019 0.001 TYR B 152 ARG 0.006 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7630 (pttm) cc_final: 0.7295 (pttm) REVERT: A 244 LEU cc_start: 0.9023 (tp) cc_final: 0.8783 (tt) REVERT: B 231 LYS cc_start: 0.7464 (pttm) cc_final: 0.7262 (pttm) REVERT: C 132 HIS cc_start: 0.8059 (p90) cc_final: 0.7067 (p90) REVERT: D 340 LYS cc_start: 0.8246 (ptmt) cc_final: 0.8042 (ptmt) outliers start: 25 outliers final: 8 residues processed: 279 average time/residue: 0.2515 time to fit residues: 110.6322 Evaluate side-chains 240 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 196 optimal weight: 0.0870 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17340 Z= 0.236 Angle : 0.623 7.707 23496 Z= 0.307 Chirality : 0.052 0.228 2640 Planarity : 0.006 0.079 2988 Dihedral : 14.270 81.717 2632 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.27 % Allowed : 9.60 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2112 helix: 0.39 (0.34), residues: 264 sheet: 0.58 (0.31), residues: 276 loop : -1.56 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.005 0.001 HIS E 338 PHE 0.014 0.001 PHE B 167 TYR 0.017 0.001 TYR B 152 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7640 (pttm) cc_final: 0.7437 (pttm) REVERT: B 167 PHE cc_start: 0.7763 (t80) cc_final: 0.7317 (t80) REVERT: B 244 LEU cc_start: 0.8853 (tp) cc_final: 0.8496 (tp) REVERT: D 340 LYS cc_start: 0.8294 (ptmt) cc_final: 0.8078 (ptmt) REVERT: E 244 LEU cc_start: 0.8924 (tp) cc_final: 0.8586 (tp) REVERT: F 66 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7381 (mp0) REVERT: F 206 PHE cc_start: 0.3906 (OUTLIER) cc_final: 0.3236 (m-80) REVERT: F 244 LEU cc_start: 0.9019 (tp) cc_final: 0.8805 (tp) outliers start: 23 outliers final: 14 residues processed: 262 average time/residue: 0.2670 time to fit residues: 108.0865 Evaluate side-chains 251 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 163 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS D 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17340 Z= 0.189 Angle : 0.564 7.200 23496 Z= 0.282 Chirality : 0.051 0.235 2640 Planarity : 0.006 0.077 2988 Dihedral : 8.036 59.055 2620 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.99 % Allowed : 11.48 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2112 helix: 0.18 (0.34), residues: 270 sheet: 0.54 (0.31), residues: 276 loop : -1.49 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 329 HIS 0.003 0.000 HIS E 338 PHE 0.012 0.001 PHE B 167 TYR 0.011 0.001 TYR A 233 ARG 0.002 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7614 (pttm) cc_final: 0.7407 (pttm) REVERT: B 47 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 66 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7566 (mt-10) REVERT: B 152 TYR cc_start: 0.7133 (p90) cc_final: 0.6743 (p90) REVERT: B 167 PHE cc_start: 0.7856 (t80) cc_final: 0.7447 (t80) REVERT: B 244 LEU cc_start: 0.8901 (tp) cc_final: 0.8553 (tp) REVERT: C 68 MET cc_start: 0.6949 (ttp) cc_final: 0.6692 (ttp) REVERT: C 131 PHE cc_start: 0.7403 (m-10) cc_final: 0.7162 (m-10) REVERT: D 168 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6440 (p) REVERT: E 167 PHE cc_start: 0.7912 (t80) cc_final: 0.7571 (t80) REVERT: E 168 VAL cc_start: 0.6892 (OUTLIER) cc_final: 0.6610 (p) REVERT: E 244 LEU cc_start: 0.8874 (tp) cc_final: 0.8573 (tp) REVERT: E 338 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7585 (t70) REVERT: F 142 MET cc_start: 0.3513 (mmm) cc_final: 0.2980 (mmt) outliers start: 36 outliers final: 11 residues processed: 281 average time/residue: 0.2669 time to fit residues: 116.2815 Evaluate side-chains 255 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS D 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17340 Z= 0.184 Angle : 0.557 8.700 23496 Z= 0.282 Chirality : 0.050 0.237 2640 Planarity : 0.006 0.077 2988 Dihedral : 6.736 58.487 2619 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.99 % Allowed : 13.74 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2112 helix: 0.18 (0.34), residues: 270 sheet: 0.44 (0.31), residues: 276 loop : -1.48 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 329 HIS 0.015 0.001 HIS B 338 PHE 0.009 0.001 PHE B 167 TYR 0.017 0.001 TYR F 152 ARG 0.003 0.000 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7479 (mt-10) REVERT: A 231 LYS cc_start: 0.7591 (pttm) cc_final: 0.7371 (pttm) REVERT: B 47 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 142 MET cc_start: 0.4731 (mmt) cc_final: 0.3961 (mmt) REVERT: B 152 TYR cc_start: 0.7023 (p90) cc_final: 0.6714 (p90) REVERT: B 167 PHE cc_start: 0.7895 (t80) cc_final: 0.7498 (t80) REVERT: B 168 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6783 (p) REVERT: B 244 LEU cc_start: 0.8889 (tp) cc_final: 0.8564 (tp) REVERT: C 66 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7561 (mt-10) REVERT: C 131 PHE cc_start: 0.7374 (m-10) cc_final: 0.7083 (m-10) REVERT: D 168 VAL cc_start: 0.6751 (OUTLIER) cc_final: 0.6527 (p) REVERT: E 68 MET cc_start: 0.7128 (ttm) cc_final: 0.6898 (ttp) REVERT: E 167 PHE cc_start: 0.7846 (t80) cc_final: 0.7595 (t80) REVERT: E 244 LEU cc_start: 0.8868 (tp) cc_final: 0.8589 (tp) REVERT: E 338 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7686 (t70) REVERT: F 66 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7167 (mp0) REVERT: F 142 MET cc_start: 0.3472 (mmm) cc_final: 0.2805 (mmt) REVERT: F 209 MET cc_start: 0.5026 (ppp) cc_final: 0.4712 (ppp) outliers start: 36 outliers final: 17 residues processed: 274 average time/residue: 0.2617 time to fit residues: 111.0597 Evaluate side-chains 259 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 239 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 155 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN E 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17340 Z= 0.326 Angle : 0.606 9.752 23496 Z= 0.308 Chirality : 0.052 0.185 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.698 58.531 2619 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.76 % Allowed : 14.85 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2112 helix: 0.02 (0.33), residues: 270 sheet: 0.27 (0.30), residues: 276 loop : -1.60 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 329 HIS 0.017 0.001 HIS B 338 PHE 0.013 0.001 PHE B 167 TYR 0.015 0.001 TYR B 233 ARG 0.004 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 257 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7498 (mt-10) REVERT: B 152 TYR cc_start: 0.7148 (p90) cc_final: 0.6830 (p90) REVERT: B 244 LEU cc_start: 0.8947 (tp) cc_final: 0.8676 (tp) REVERT: B 283 ASP cc_start: 0.8161 (m-30) cc_final: 0.7925 (m-30) REVERT: B 338 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7337 (t-90) REVERT: E 244 LEU cc_start: 0.8899 (tp) cc_final: 0.8679 (tp) REVERT: E 283 ASP cc_start: 0.8150 (m-30) cc_final: 0.7912 (m-30) REVERT: E 338 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7726 (t70) REVERT: F 142 MET cc_start: 0.3401 (mmm) cc_final: 0.2823 (mmt) outliers start: 50 outliers final: 34 residues processed: 297 average time/residue: 0.2752 time to fit residues: 124.8417 Evaluate side-chains 289 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 0.0010 chunk 96 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17340 Z= 0.168 Angle : 0.553 10.093 23496 Z= 0.282 Chirality : 0.050 0.176 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.317 59.662 2619 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 1.99 % Allowed : 16.56 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2112 helix: 0.18 (0.35), residues: 264 sheet: 0.41 (0.31), residues: 276 loop : -1.53 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.005 0.000 HIS B 338 PHE 0.014 0.001 PHE E 167 TYR 0.019 0.001 TYR C 152 ARG 0.004 0.000 ARG F 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7593 (mt-10) REVERT: B 9 MET cc_start: 0.5681 (tpt) cc_final: 0.5461 (tpp) REVERT: B 47 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 142 MET cc_start: 0.4430 (mmt) cc_final: 0.3817 (mmt) REVERT: B 244 LEU cc_start: 0.8899 (tp) cc_final: 0.8581 (tp) REVERT: B 305 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8222 (mm) REVERT: E 9 MET cc_start: 0.5077 (tpp) cc_final: 0.4765 (tpp) REVERT: E 244 LEU cc_start: 0.8868 (tp) cc_final: 0.8598 (tp) REVERT: E 305 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (mm) REVERT: E 321 MET cc_start: 0.7853 (ttm) cc_final: 0.7628 (ttm) REVERT: E 338 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7539 (t70) REVERT: F 66 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7406 (mp0) REVERT: F 102 ARG cc_start: 0.7557 (ptt-90) cc_final: 0.7325 (ptp90) outliers start: 36 outliers final: 25 residues processed: 274 average time/residue: 0.2778 time to fit residues: 115.7349 Evaluate side-chains 274 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 246 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.0470 chunk 23 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 130 optimal weight: 0.0040 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.0010 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN F 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 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 : 0.002 0.031 17340 Z= 0.151 Angle : 0.538 9.788 23496 Z= 0.274 Chirality : 0.049 0.167 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.080 58.600 2619 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.15 % Allowed : 16.50 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2112 helix: 0.23 (0.35), residues: 264 sheet: 0.49 (0.31), residues: 276 loop : -1.47 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 329 HIS 0.002 0.000 HIS E 338 PHE 0.013 0.001 PHE E 167 TYR 0.019 0.001 TYR B 152 ARG 0.010 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 253 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7546 (mt-10) REVERT: B 9 MET cc_start: 0.5625 (tpt) cc_final: 0.5411 (tpp) REVERT: B 142 MET cc_start: 0.4351 (mmt) cc_final: 0.4053 (mmt) REVERT: B 167 PHE cc_start: 0.7362 (t80) cc_final: 0.7138 (t80) REVERT: B 244 LEU cc_start: 0.8888 (tp) cc_final: 0.8551 (tp) REVERT: B 305 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 338 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: D 142 MET cc_start: 0.3416 (mtp) cc_final: 0.2980 (mtt) REVERT: D 209 MET cc_start: 0.4979 (ptm) cc_final: 0.4500 (ptt) REVERT: E 9 MET cc_start: 0.5118 (tpp) cc_final: 0.4811 (tpp) REVERT: E 142 MET cc_start: 0.4441 (mtp) cc_final: 0.4233 (mmt) REVERT: E 209 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.4817 (ppp) REVERT: E 244 LEU cc_start: 0.8840 (tp) cc_final: 0.8554 (tp) REVERT: E 305 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8146 (mm) REVERT: E 338 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7331 (t70) REVERT: F 66 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7404 (mp0) outliers start: 39 outliers final: 27 residues processed: 277 average time/residue: 0.2670 time to fit residues: 114.9783 Evaluate side-chains 279 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.0010 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.0870 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17340 Z= 0.159 Angle : 0.541 11.531 23496 Z= 0.272 Chirality : 0.049 0.188 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.954 58.060 2619 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.10 % Allowed : 16.78 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2112 helix: 0.18 (0.35), residues: 264 sheet: 0.10 (0.28), residues: 348 loop : -1.50 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 329 HIS 0.002 0.000 HIS E 338 PHE 0.009 0.001 PHE F 131 TYR 0.026 0.001 TYR E 152 ARG 0.003 0.000 ARG F 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7515 (mt-10) REVERT: B 244 LEU cc_start: 0.8877 (tp) cc_final: 0.8552 (tp) REVERT: B 305 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8162 (mm) REVERT: B 338 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7447 (t-90) REVERT: D 142 MET cc_start: 0.3315 (mtp) cc_final: 0.2730 (mtt) REVERT: E 244 LEU cc_start: 0.8825 (tp) cc_final: 0.8535 (tp) REVERT: E 305 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (mm) REVERT: E 338 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7286 (t70) REVERT: F 66 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7420 (mp0) outliers start: 38 outliers final: 27 residues processed: 278 average time/residue: 0.2721 time to fit residues: 116.4836 Evaluate side-chains 275 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 0.2980 chunk 194 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 152 optimal weight: 0.0470 chunk 59 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 chunk 193 optimal weight: 8.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17340 Z= 0.165 Angle : 0.556 12.401 23496 Z= 0.278 Chirality : 0.049 0.185 2640 Planarity : 0.006 0.083 2988 Dihedral : 5.923 57.089 2619 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.88 % Allowed : 17.33 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2112 helix: 0.25 (0.35), residues: 264 sheet: 0.11 (0.28), residues: 348 loop : -1.51 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 329 HIS 0.002 0.000 HIS E 338 PHE 0.008 0.001 PHE C 131 TYR 0.023 0.001 TYR B 152 ARG 0.010 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7525 (mt-10) REVERT: B 244 LEU cc_start: 0.8866 (tp) cc_final: 0.8541 (tp) REVERT: B 305 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 338 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: D 142 MET cc_start: 0.3475 (mtp) cc_final: 0.2981 (mtt) REVERT: E 244 LEU cc_start: 0.8818 (tp) cc_final: 0.8521 (tp) REVERT: E 305 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8134 (mm) REVERT: E 338 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7295 (t70) REVERT: F 66 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7410 (mp0) REVERT: F 142 MET cc_start: 0.3499 (mmm) cc_final: 0.2884 (mmt) outliers start: 34 outliers final: 26 residues processed: 266 average time/residue: 0.2708 time to fit residues: 110.7578 Evaluate side-chains 273 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17340 Z= 0.202 Angle : 0.565 12.922 23496 Z= 0.283 Chirality : 0.049 0.173 2640 Planarity : 0.006 0.077 2988 Dihedral : 5.982 56.980 2619 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.77 % Allowed : 17.33 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2112 helix: 0.43 (0.36), residues: 252 sheet: 0.09 (0.28), residues: 348 loop : -1.53 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 329 HIS 0.003 0.001 HIS E 338 PHE 0.014 0.001 PHE F 131 TYR 0.020 0.001 TYR E 152 ARG 0.007 0.000 ARG B 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7552 (mt-10) REVERT: B 244 LEU cc_start: 0.8883 (tp) cc_final: 0.8578 (tp) REVERT: B 338 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: D 142 MET cc_start: 0.3563 (mtp) cc_final: 0.2960 (mtt) REVERT: E 209 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.4856 (ppp) REVERT: E 244 LEU cc_start: 0.8841 (tp) cc_final: 0.8551 (tp) REVERT: E 305 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8136 (mm) REVERT: E 338 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7438 (t70) REVERT: F 66 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7442 (mp0) outliers start: 32 outliers final: 27 residues processed: 262 average time/residue: 0.2578 time to fit residues: 104.2886 Evaluate side-chains 272 residues out of total 1812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 241 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 25 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.191985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161945 restraints weight = 18110.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151037 restraints weight = 24010.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150939 restraints weight = 21060.478| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17340 Z= 0.193 Angle : 0.572 12.497 23496 Z= 0.284 Chirality : 0.049 0.172 2640 Planarity : 0.006 0.077 2988 Dihedral : 5.983 58.096 2619 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.04 % Allowed : 17.60 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2112 helix: 0.43 (0.36), residues: 252 sheet: 0.11 (0.28), residues: 348 loop : -1.54 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 329 HIS 0.003 0.000 HIS E 338 PHE 0.011 0.001 PHE F 240 TYR 0.021 0.001 TYR B 152 ARG 0.005 0.000 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.40 seconds wall clock time: 60 minutes 59.13 seconds (3659.13 seconds total)